| NCBI, EMBL, DDBJ |
|
| Site Name |
Description |
Clicks |
| NCBI Home Page |
It is a vast repository and a public database of nucleic acid sequences, literature and genome specific resources. Besides, it provides several biocomputational tools for sequence analysis and FTPs for sequence retreival. The various databases harbored by NCBI are "PubMed (biomedical literature citations and abstracts), PubMed Central (free, full text journal articles), Site Search (NCBI web and FTP sites), Books (online books), OMIM (online Mendelian Inheritance in Man ), Nucleotide (Core subset of nucleotide sequence records), EST (Expressed Sequence Tag records), GSS (Genome Survey Sequence records), Protein (sequence database), Genome (whole genome sequences), Structure (three-dimensional macromolecular structures), Taxonomy (organisms in GenBank), SNP (short genetic variations), dbVar (Genomic structural variation), Gene (gene-centered information), SRA (Sequence Read Archive), BioSystems (Pathways and systems of interacting molecules), HomoloGene (eukaryotic homology groups), Probe (sequence-specific reagents), BioProject (aggregated biological research project data ), dbGaP (genotype and phenotype), UniGene (gene-oriented clusters of transcript sequences), CDD (conserved protein domain database), Clone (integrated data for clone resources), UniSTS (markers and mapping data), PopSet (population study data sets), GEO Profiles (expression and molecular abundance profiles ), GEO DataSets (experimental sets of GEO data), Epigenomics (Epigenetic maps and data sets), PubChem BioAssay (bioactivity screens of chemical substances), PubChem Compound (unique small molecule chemical structures), PubChem Substance (deposited chemical substance records ), Protein Clusters (a collection of related protein sequences), OMIA (online Mendelian Inheritance in Animals), BioSample (biological material descriptions ), NLM Catalog (catalog of books, journals, and audiovisuals in the NLM collections) and MeSH (detailed information about NLM's controlled vocabulary)". |
3696 |
| NCBI-dbVar |
dbVar is a database maintained by NCBI for "genomic structural variations". |
3677 |
| GenBank |
A public repository of nucleotide sequences provided by NCBI. |
3248 |
| NCBI Human Genome Browser |
"The NCBI Map Viewer provides graphical displays of features on the human reference genome sequence assembly maintained by the GRC and the alternate HuRef genome assembly, as well as cytogenetic, genetic, physical, and radiation hybrid maps. Map features can be seen along the sequence include genes, transcripts, NCBI contigs (the 'Contig' map), the BAC tiling path (the 'Component' map), STSs, FISH mapped clones, ESTs and transcripts from several different organisms, Gnomon predicted gene models" etc. |
3249 |
| NIH Human Microbiome Project |
The Human Microbiome Project (HMP) is the initiative of United States National Institutes of Health "with the goal of identifying and characterizing the microorganisms which are found in association with both healthy and diseased humans". |
3604 |
| Entrez |
"PubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites". |
3110 |
| NCBI GenBank Taxonomy Database |
It provides taxonomical information of an organism (used in molecular biology research work). |
4702 |
| EMBL-EBI |
The EBI, a part of EMBL, is an academic research institute located on the Wellcome Trust Genome Campus in Cambridge (UK). It serves as a public repository of molecular data. It also provides free online bioinformatic software and tools. |
3888 |
| EMBL |
"The EMBL Nucleotide Sequence Database (also known as EMBL-Bank) constitutes Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications". |
5216 |
| DDBJ |
"The DNA Databank of Japan is one of the three summit databank that construct DDBJ/EMBL/GenBank International Nucleotide Sequence database through close collaboration of EBI in Europe and NCBI in USA". |
3416 |
| Transcriptional Regulatory Element Database |
This database is a good resource to obtain training datasets for genome wide cis-regulatory element prediction, gene functional studies, and exploring gene regulatory networks |
2991 |
| Promoter Analysis Pipeline (PAP) |
It is used for analyzing set of coexpressed genes vis-a-vis predicting the transcriptional regulatory mechanisms |
2943 |
| STACK |
"The STACKdb, Sequence Tag Alignment and Consensus Knowledgebase, is generated by processing EST and mRNA sequences obtained from GenBank through a pipeline consisting of masking, clustering, alignment and variation analysis steps" |
2756 |
| ENA Sequence Verion Archive |
The ENA Sequence Version Archive is a repository of all entries which have ever appeared in EMBL-Bank Sequence Database. |
3019 |
| Clusters of orthologous groups of proteins (NCBI) |
"The COG protein database was generated by comparing predicted and known proteins in all completely sequenced microbial genomes to infer sets of orthologs. Each COG consists of a group of proteins found to be orthologous across at least three lineages and likely corresponds to an ancient conserved domain" |
3567 |
| Entrez Gene |
"Entrez Gene is NCBI's repository for gene-specific information" |
2643 |
| OMIA |
"Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and genes in 215 animal species (other than human and mouse and rats, which have their own resources)". "OMIA information is stored in a database that contains textual information and references, as well as links to relevant PubMed and Gene records at the NCBI, and to OMIM and Ensembl" |
2640 |
| Homophila |
"Homophila utilizes the sequence information of human disease genes from the NCBI OMIM (Online Mendelian Inheritance in Man) database in order to determine if sequence homologs of these genes exist in the current Drosophila sequence database (FlyBase). Sequences are compared using NCBI's BLAST program. The database is updated weekly and can be searched by human disease, gene name, OMIM number, title, subtitle and/or allelic variant descriptions" |
2711 |
| PubChem |
"This database provides comprehensive search facilities for finding a particular component, or determining components in structure entries or vice versa." |
2560 |
| DDBJ Search and analysis tools |
This is DDBJ page that contains several tols for Database search, Genome Analysis, NGS Analysis, Phylogenetics, Submission of gene expression data, Protein Dtatabase and structure etc. |
3432 |
| NCBI RefSeq |
"A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein" |
3904 |
| dbSNP |
"The Database of Short Genetic Variation (dbSNP) is a public archive of all short sequence variation and includes a broad collection of simple genetic variations such as single-base nucleotide substitutions, small-scale multi-base deletions or insertions, and microsatellite repeats" |
2954 |
| OMIM |
It is an "Online Catalog of Human Genes and Genetic Disorders" |
2877 |
|
Top of Page
| Protein Databases |
|
| Site Name |
Description |
Clicks |
| PDB |
"The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards". |
3322 |
| Pfam |
"The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models" . |
2961 |
| PIR |
"The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information". |
3896 |
| PROSITE |
"PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them . PROSITE is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids". |
3122 |
| SWISSPROT- TrEMBL |
It is "a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases". |
3821 |
| RCSB |
The Research Collaboratory for Structural Bioinformatics (RCSB) undertakes research works directed towards understanding the “function of biological systems through the study of the 3-D structure of biological macromolecules”. |
2959 |
| Emotif Software |
"The EMOTIF database is a collection of more than 170 000 highly specific and sensitive protein sequence motifs representing conserved biochemical properties and biological functions". E-MOTIF package is downloadable and installable. |
2864 |
| Kabat |
"The Kabat Database contains aligned immunoglobulin superfamily sequences collected over the course of 30 years. The Kabat Database is unique in that a majority of the immunoglobulin sequences in it were manually culled from the scientific literature, entered and aligned by hand, long before the advent of nearly all familiar genomic databases". |
3079 |
| Blocks |
"Blocks are multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins. Block Searcher, Get Blocks and Block Maker are aids to detection and verification of protein sequence homology". |
2760 |
| PRINTS |
"PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite". |
2835 |
| ProDom |
"ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database". |
3063 |
| InterPro |
"InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites". |
6062 |
| Multiple EM for Motif Elicitation (MEME) |
"MEME is a tool for discovering motifs in a group of related DNA or protein sequences". |
2806 |
| Motif Alignment & Search Tool |
A program (developed by Bailey & Gribskov, 1997) is used to find the most probable order and spacing of the patterns. |
2778 |
| SMART |
SMART is a classification scheme for identifying and analysing protein domains. The database is maintaineded by the EMBL (Heidelberg). |
3079 |
| GTOP |
"GTOP is a database consisting of data analyses of proteins identified by various genome projects. This database mainly uses sequence homology analyses and features extensive utilization of information on three-dimensional structures" |
2592 |
| PASS2 |
"PASS2 is an automatic version of the original superfamily alignment database and contains alignments of protein structures at the superfamily level and is in direct correspondence with SCOP 1.75 release (Structural Classification Of Proteins, Murzin et al.,1995)." |
2583 |
| ADDA |
"ADDA is an automatic algorithm for domain decomposition and clustering of all protein domain familie that uses alignments derived from an all-on-all sequence comparison to define domains within protein sequences based on a global maximum likelihood model." |
2514 |
| FunShift |
"FunShift provides Functional shift (divergence) analysis between the subfamilies of a Protein domain family." |
2525 |
| APD |
"Antimicrobial Peptide Database and data analysis system (APD) develops the antimicrobial peptide database into a comprehensive tool for discovery timeline, naming (nomenclature), classification, information search, statistical analysis, prediction, and design of antimicrobial peptides covering all life kingdoms (bacteria, protozoa, fungi, plants, and animals)" |
2628 |
| ANTIMIC |
"Antimicrobial Peptide Database and data analysis system (APD) develops the antimicrobial peptide database into a comprehensive tool for discovery timeline, naming (nomenclature), classification, information search, statistical analysis, prediction, and design of antimicrobial peptides covering all life kingdoms (bacteria, protozoa, fungi, plants, and animals)" |
3266 |
| ASTRAL |
"The ASTRAL compendium provides databases and tools useful for analyzing protein structures and their sequences." |
3112 |
| TOPS |
"TOPS motifs are fragments of TOPS diagrams that are shared by several proteins (domains) believed to have some biological relationship together with some biological annotaion." |
2619 |
| Blocks |
"Blocks are multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins. Block Searcher, Get Blocks and Block Maker are aids to detection and verification of protein sequence homology. They compare a protein or DNA sequence to a database of protein blocks, retrieve blocks, and create new blocks, respectively." |
2556 |
| eBLOCKS |
"The Blocks Database contains multiple alignments of conserved regions in protein families." |
2576 |
| SIMAP |
"SIMAP is a database of protein similarities and protein domains. " |
2651 |
| DSDBASE |
"DSDBASE is a database of disulphide bonds in proteins, which provides information on native disulphides and those that are stereochemically possible between pairs of residues for all known protein structural entries. " |
2567 |
| GenDiS |
"Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases" |
2500 |
| CKAAPs DB |
"The Conserved Key Amino Acid Positions DataBase (CKAAPs DB) provides access to an analysis of structurally similar proteins with dissimilar sequences where key residues within a common fold are identified." |
2464 |
| CADB |
"Conformation Angles DataBase [ CADB-3.0 ] is a comprehensive, authoritative and timely knowledge base developed to facilitate retrieval of information related to the conformational angles (main-chain and side-chain) of the amino acid residues present in the non-redundant (both 25% and 90%) data set." |
2532 |
| Decoys 'R' Us |
"Decoys are computer generated conformations of protein sequences that possess some characteristics of native proteins, but are not biologically real. The primary use of decoys is to test scoring, or energy, functions" |
2563 |
| eF-site |
"eF-site (electrostatic-surface of Functional site) is a database for molecular surfaces of proteins' functional sites, displaying the electrostatic potentials and hydrophobic properties together on the Connolly surfaces of the active sites, for analyses of the molecular recognition mechanisms." |
2481 |
| Dali |
"The Dali Database is based on all-against-all 3D structure comparison of protein structures in the Protein Data Bank (PDB)." |
2501 |
| FSN |
"Flexible Structural Neighborhood (FSN), a database of structural neighbors of proteins deposited in PDB as seen by a flexible protein structure alignment program FATCAT" |
2627 |
| GTD |
"Gene3D is primarily a database of CATH v4.0 protein domain assignments for ENSEMBL and UniProt sequences" |
2713 |
| LPFC |
"LPFC is a database of structural alignments of protein families and computed average core structures for each family." |
2586 |
| Het-PDB Navi |
"Het-PDB Navi. is a navigator of small molecules in Protein Data Bank which is called heterogen atoms or in short hetatoms." |
2773 |
| Hits |
"Hits is a free database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them. These motifs are defined by an heterogeneous collection of predictors, which currently includes regular expressions, generalized profiles and hidden Markov models." |
2639 |
| MulPSSM |
"Representation of multiple sequence alignments of protein families in terms of Position Specific Scoring Matrices (PSSMs) is commonly used in the detection of remote homologues." |
2529 |
| Protein-protein interfaces |
"This includes the survey of the structures of protein-protein interfaces in PDB to carry out the structural comparisons of the interfaces." |
2925 |
| InterDom |
"InterDom is a database of putative interacting protein domains derived from multiple sources, ranging from domain fusions (Rosetta Stone), protein interactions (DIP and BIND), protein complexes (PDB), to scientific literature (MEDLINE). " |
2626 |
| LEGER |
"The Proteome database LEGER was developed to support functional genome analyses by combining information obtained by applying bioinformatics methods and from public databases to improve the original annotations" |
2516 |
| LOCATE |
"LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set." |
2643 |
| eMOTIF |
"The EMOTIF database is a collection of more than 170 000 highly specific and sensitive protein sequence motifs representing conserved biochemical properties and biological functions. " |
2453 |
| Xpro |
"Xpro is a relational database that contains all the eukaryotic protein-encoding DNA sequences in GenBank." |
2457 |
| PDB TM |
"PDBTM is the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank (PDB)." |
2807 |
| Peptaibol |
"Peptaibols generally exhibit antimicrobial activity and are referred to as antibiotic peptides. The main sources of the peptaibols known to date are fungii of the genre Trichoderma and Emericellopsis. Peptidabol database is A Bioinformatics resource from the School of Crystallography" |
2524 |
| Pfam |
"The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). " |
2510 |
| Phospho. ELM |
"Phospho.ELM is a database of experimentally verified phosphorylation sites in eukaryotic proteins." |
2781 |
| iProClass |
"The iProClass database provides value-added information reports for UniProtKB and unique NCBI Entrez protein sequences in UniParc, with links to over 175 biological databases, including databases for protein families, functions and pathways, interactions, structures and structural classifications, genes and genomes, ontologies, literature, and taxonomy." |
2659 |
| PIR-NREF |
"The Protein Information Resource (PIR) is an integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies." |
2824 |
| PMD |
"The Protein Mutant Database (PMD) that we are constructing covers natural as well as artificial mutants, including random and site-directed ones, for all proteins except members of the globin and immunoglobulin families" |
2493 |
| ProDom |
"ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database" |
2463 |
| DSMM |
"Database of Simulated Molecular Motions (DSMM) .The purpose of this database is to provide an easily-searchable source of information about movies showing biomolecular motions that have been generated by computer simulation." |
2491 |
| Gene3D |
"Gene3D is a database for Structural and Functional Annotation of Protein Families" |
2681 |
| REFOLD |
"REFOLD is a web-accessible relational database containing the published methods employed in the refolding of recombinant proteins." |
2547 |
| ArchDB |
"ArchDB is a structural classification of loops extracted from known protein structures." |
2677 |
| SCOP |
"The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of known protein structures. " |
3383 |
| SMART |
"SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures" |
3005 |
| SPD |
"SPD, Secreted Protein Database is a collection of secreted proteins from Human, Mouse and Rat proteomes, which includes sequences from SwissProt, Trembl, Ensembl and Refseq" |
2485 |
| GTOP |
"GTOP is a database consisting of data analyses of proteins identified by various genome projects. This database mainly uses sequence homology analyses and features extensive utilization of information on three-dimensional structures." |
2430 |
| SUPFAM |
"This database consists of clusters of potentially related homologous protein domain families, with and without three-dimensional structural information, forming superfamilies." |
2571 |
| PDBBIND |
" The PDBbind database is designed to provide a collection of experimentally measured binding affinity data (Kd, Ki, and IC50) exclusively for the protein-ligand complexes available in the Protein Data Bank (PDB)." |
2484 |
| SYSTERS |
"SYSTERS (short for SYSTEmatic Re-Searching) is a collection of graph-based algorithms to hierarchically partition a large set of protein sequences into homologous families and superfamilies" |
4549 |
| HOMSTRAD |
"HOMSTRAD (HOMologous STRucture Alignment Database) is a curated database of structure-based alignments for homologous protein families. " |
2512 |
| PA-GOSUB |
"The Proteome Analyst Specialized Subcellular Localization Server (PA-SUB) is part of Proteome Analyst (PA) which is a web server built to predict protein properties, such as general function, in a high-throughput fashion. PA-SUB is specialized to predict the subcellular localization of proteins using established machine learning techniques." |
2779 |
| Metalloprotein site |
"Metalloprotein site Database and Browser (MDB) contains quantitative information on all the metal-containing sites available from structures in the PDB distribution. This database contains geometrical and molecular information that allows the classification and search of particular combinations of site characteristics," |
2241 |
| PepConfDB |
"A database of peptide conformations. " |
2442 |
| PDB |
"RCSB PDB is used to perform simple and advanced searches based on annotations relating to sequence, structure and function, and to visualize, download, and analyze molecules." |
3476 |
| ProTherm |
"ProTherm is a collection of numerical data of thermodynamic parameters such as Gibbs free energy change, enthalpy change, heat capacity change, transition temperature etc. for wild type and mutant proteins, that are important for understanding the structure and stability of proteins" |
2459 |
| AffinDB |
"The Affinity Database 'AffinDB' contains affinity data for protein-ligand complexes of the PDB. Its purpose is to provide direct and free access to the experimental affinity of a given complex structure." |
2578 |
| PRINTS |
"PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite." |
2604 |
| DBSubLoc |
"DBSubLoc is a database of protein subcellular localization. This database contains proteins from primary protein database SWISS-PROT and PIR" |
2578 |
| BioMagResBank |
"Biological magnetic resonance databank is a Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules" |
2683 |
| IMOTdb |
"The interacting motif database or iMOTdb , lists interacting motifs thatare identified for all structural entries in the PDB. The conserved patterns or finger prints are identified for individual structural entries and also grouped together for reporting the common motifs shared among all superfamily members." |
2519 |
| PMDB |
"The Protein Model Database (PMDB) is a public resource aimed at storing manually built 3D models of proteins. The database is designed to provide access to models published in the scientific literature, together with validating experimental data" |
2515 |
| CATH |
"The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank." |
3837 |
| STING Report |
"The Sting Report is a versatile web-based application for extraction and presentation of detailed information about any individual amino acid of a protein structure stored in the STING Database" |
2473 |
| SURFACE |
"The SURFACE (SUrface Residues and Functions Annotated, Compared and Evaluated) database is a repository of annotated and compared protein surface regions" |
2433 |
| NESbase |
"NESbase is a database of proteins in which the presence of Leucine-rich nuclear export signal (NES) has been experimentally verified. It is curated from literature." |
2486 |
| O-GlycBase |
"O-GLYCBASE is a revised database of O- and C-glycosylated proteins. " |
2651 |
| DomIns |
"DomIns: A Web Resource for Domain Insertions in Known Protein Structures" |
2527 |
| PDBsum |
"PDBsum is a pictorial database that provides an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank (PDB). It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of the interactions between them. " |
2392 |
| InterPro |
"InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites." |
3149 |
| CluSTr |
"The CluSTr database offers an automatic classification of UniProt Knowledgebase and IPI proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons (Smith-Waterman) between protein sequences." |
2447 |
| PRO SITE |
"PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them" |
2413 |
| Swiss-Prot |
"UniProtKB/Swiss-Prot is a high quality annotated and non-redundant protein sequence database, which brings together experimental results, computed features and scientific conclusions." |
2555 |
| TrEMBL |
"UniProtKB/TrEMBL is a computer-annotated protein sequence database that contains the translations of all coding sequences (CDS) present in the EMBL/GenBank/DDBJ Nucleotide Sequence Databases and also protein sequences extracted from the literature or submitted to UniProtKB/Swiss-Prot." |
2309 |
| ProRule |
"ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc." |
2415 |
| LIGAND |
" It is a composite database consisting of COMPOUND, GLYCAN, REACTION, RPAIR, RCLASS, and ENZYME databases, whose entries are identified by C, G, R, RP, RC, and EC numbers, respectively." |
2784 |
| AAindex |
"AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids." |
2947 |
| TMPDB |
"This database was used as the test data set of the paper describing TSEG (Prediction Tool for Transmembrane SEGments in proteins)." |
2504 |
| SBASE |
"SBASE is a collection of protein domain sequences collected from the literature, from protein sequence databases and from genomic databases " |
2309 |
| PDB-Ligand |
"PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures." |
2610 |
| IMGT/3Dstructure-DB |
"IMGT/3Dstructure-DB contains information on the sequences, 2D structures (or Colliers de Perles) and 3D structures of IG, TR and MHC and related proteins of the immune system (RPI) with known 3D structures, from human and other vertebrate species. Experimental 3D data are from PDB. Expertly annotated information is provided according to the IMGT-ONTOLOGY concepts and to the IMGT Scientific chart rules." |
2440 |
| TIGRFAMs |
"TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins." |
2600 |
| NOPdb |
"Nucleolar Proteome Database site contains all of the data from our ongoing proteomic analysis of human nucleoli," |
2384 |
| TransportDB |
It "is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available. For each organism, its complete membrane transport complement was identified, classified into protein families according to the TC classification system, and functional predictions are provided" |
3030 |
| MIPS |
"The Munich Information Center for Protein Sequences (MIPS) provides genome-related information in a systematic way. It develops and maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences, and provides tools for the comprehensive analysis of protein sequences." |
2267 |
| CDD |
"CDD is a protein annotation resource that consists of a collection of well-annotated multiple sequence alignment models for ancient domains and full-length proteins." |
4942 |
| Protein Folding database |
"Protein Folding Database (PFD) is a searchable repository of freely available experimental protein folding data." |
2502 |
| PIRSF |
"The Protein Information Resource (PIR) is an integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies " |
2340 |
| PIR-ALN |
"The database includes alignments of protein sequences that represent superfamilies, families, and homology domains." |
2423 |
| PPD |
"Plasma Proteome Database (PPD) was developed as a part of Human Proteome Organization's (HUPO) initial effort to characterize human plasma proteome. " |
2865 |
| PRF |
"The Peptide Institute, Protein Research Foundation collects the information related to amino acids, peptides and proteins and make databases." |
2747 |
| ProTeus |
"ProTeus (PROtein TErminUS) is a tool for identification of short linear signatures in protein termini. It is based on a positional-based search method for revealing short significant signatures in termini of proteins." |
2447 |
| ProtoNet |
"ProtoNet provides automatic hierarchical classification of protein sequences." |
2251 |
| ModBase |
"ModBase is a database of comparative protein structure models, calculated by the modeling pipeline ModPipe." |
2443 |
| ProtoMap |
"PROTOMAP is a recently developed technique to map in vivo substrates of proteolytic events. PROTOMAP uses 1D SDS-PAGE and mass spectrometry to globally identify shifts in gel-migration and corresponding changes in the topography of proteolytic fragments" |
2453 |
| SUPERFAMILY |
"SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes." |
2559 |
| SWISS-MODEL |
"The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL." |
3987 |
| Repository target DB |
"TargetTrack, a target registration database, provides information on the experimental progress and status of targets selected for structural determination by the Protein Structure Initiative and other worldwide high-throughput structural biology projects." |
2489 |
| UniRef |
"The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms)" |
4137 |
| UniProt |
" UniProt provides the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information." |
2283 |
| Sloop |
"Sloop Database ñ Sloop Database of Super Secondary Fragments is a classification of protein loops" |
2336 |
| PDBSite |
"The Protein Data Bank (PDB) contains data on the spatial protein structures and their biologically active sites (i.e., ligand binding regions, enzyme catalytic centers, regions subjected to biochemical modifications, etc.)" |
2553 |
| NLSdb |
"NLSdb is a database of nuclear localization signals (NLSs) and of nuclear proteins targeted to the nucleus by NLS motifs" |
2653 |
| NCBI Protein database |
"Gquery refers to Global Cross Database NCBI search that provides access to biomedical and genomic information." |
2392 |
| NMPdb |
"NMP-db is a database of nuclear matrix associated proteins" |
2549 |
| PDB-REPRDB |
"PDB-REPRDB is a reorganized database of protein chains from PDB(Protein Data Bank),and provides 'the list of the representative protein chains' and the list of similar protein chain groups'." |
2903 |
| EXProt |
"EXProt (database for EXPerimentally verified Protein functions) is a non-redundant database containing protein sequences for which the function has been experimentally verified." |
2417 |
| DisProt |
"The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part." |
2379 |
| UniParc |
"The UniProt Archive (UniParc) is a comprehensive and non-redundant database that contains most of the publicly available protein sequences in the world." |
2415 |
|
Top of Page
| RNA Databases |
|
| Site Name |
Description |
Clicks |
| The RNAdb |
"This database is a comprehensive mammalian noncoding RNA database (RNAdb) containing sequences and annotations for tens of thousands of noncoding RNAs. These include a wide range of microRNAs, small nucleolar RNAs and larger mRNA-like ncRNAs". |
2770 |
| Comparative RNA database |
"The Comparative RNA Web (CRW) Site disseminates information about RNA structure and evolution that has been determined using comparative sequence analysis". |
2872 |
| Genomic tRNA database |
“This genomic tRNA database contains tRNA gene predictions made by the program tRNAscan-SE on complete or nearly complete genomes”. |
3788 |
| European rRNA database |
"This database compiles all complete or nearly complete SSU (small subunit) and LSU (large subunit) ribosomal RNA sequences", in aligned format. "The alignment takes into account the secondary structure information derived by comparative sequence analysis". |
2747 |
| miRNA Database |
"The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR)" |
4705 |
| RNABase |
"RNABase is a unified database of all three-dimensional structures containing RNA deposited in either the Protein Data Bank (PDB) or Nucleic Acid Data Base (NDB)." |
2597 |
| ASRP |
"The ASRP database provides a repository for sequences of small RNAs cloned from various Arabidopsis genotypes and tissues." |
2474 |
| HyPaLib |
"The database, called HyPaLib (for Hybrid Pattern Library), contains annotated structural elements characteristic for certain classes of structural and/or functional RNAs." |
2285 |
| ncRNAs Database |
"The noncoding RNA (ncRNA) database is intended to provide information on the sequences and functions of transcripts which do not code for proteins, but perform regulatory roles in the cell." |
2506 |
| European rRNA data-base |
"European ribosomal RNA database compiles all complete or nearly complete SSU (small subunit) and LSU (large subunit) ribosomal RNA sequences." |
2655 |
| vRSDB |
"GRSDB2 is a second generation database of G-quadruplexes. It contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including that are alternatively processed (alternatively spliced or alternatively polyadenylated)." |
2557 |
| tm RNA website |
"tmRNA is a bacterial RNA molecule with dual tRNA-like and mRNA-like properties.This database contains 1631 unique sequences and links these to 12509 instances in GenBank/ENA/DDBJ (INSDC) entries that comprise 7590 taxa." |
2509 |
| RNAi Codex |
"Codex provides a platform to collect and search short-hairpin RNA constructs (shRNAs) used for forward genetic screens." |
2517 |
| 16S rRNA database |
"A 16S rRNA gene database addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies." |
2753 |
| Transterm |
"Transterm is a database providing access to mRNA sequences and associated regulatory elements." |
2728 |
| Small RNA Database |
"The small RNA database is a compilation of all the small size RNA sequences available to date, including nuclear, nucleolar, cytoplasmic and mitochondria small RNAs from eukaryotic organisms and small RNAs from prokaryotic cells as well as viruses." |
2475 |
| MeRNA |
"MeRNA is a comprehensive compilation of all metal binding sites identified in RNA 3D structures available from the PDB and Nucleic Acid Database." |
2468 |
| MODOMICS |
"MODOMICS presents RNA modification pathways on the level of nucleosides," |
2724 |
| RNA Modification database |
"The RNA modification database provides a comprehensive listing of posttranscriptionally modified nucleosides from RNA" |
2599 |
| Yeast snoRNA Database |
"Small Nucleolar RNAs (snoRNAs) from the Yeast Saccharomyces cerevisiae is a comprehensive database of S. cerevisiae H/ACA and C/D box snoRNAs." |
2467 |
| PolyA DB |
"PolyA_DB is a web resource for analysis of pre-mRNA cleavage and polyadenylation sites (polyA sites)" |
2336 |
| RNA-DB |
"RNAdb 2.0 is a database of mammalian noncoding RNAs" |
2320 |
| 5S rRNA Database |
"The purpose of this database is to provide information on nucleotide sequences of 5S rRNAs and their genes. The sequences for particular organisms can be retrieved as single files using a taxonomic browser or in multiple sequence structural alignments." |
2448 |
| RRNDB |
"The Ribosomal RNA Operon Copy Number Database (rrndb) is an Internet-accessible database containing annotated information on rRNA operon copy number among prokaryotes." |
2372 |
| siRNAdb |
" The siRNA database provides a gene-centric view of siRNA experimental data, including siRNAs of known efficacy and siRNAs predicted to be of high efficacy by a combination of methods." |
2380 |
| Subviral RNA database |
"This is an online database containing a large number of sequences and related data on viroids, viroid-like RNAs and human hepatitis delta virus (vHDV) in a customizable and user-friendly format." |
2474 |
| ISSD |
"ISSD serves as an integrated source of sequence and structure information for the analysis of correlations between mRNA synonymous codon usage and threedimensional structure of the encoded proteins." |
2313 |
| tRNA Sequences |
"tRNAdb provides a powerful and fast search engine. Taxons can be identified by browsing the taxonomic tree or by using the search form. Queries can include DNA or RNA sequences, amino acid family, anticodon, references, Pubmed-ID of the reference, gene ID as well as comments." |
2557 |
| Guide RNA Database |
"The gRNA database currently contains 250 guide RNA sequences as well as secondary and tertiary structure models and other relevant information." |
2370 |
| Plant snoRNA DB |
"The plant snoRNA Database and web-site brings together information from three independent computer-assisted searches of the Arabidopsis genome for box C/D snoRNA genes and from studies of ncRNAs." |
2299 |
| NPInter |
"NPInter documents functional interactions between noncoding RNAs (except tRNAs and rRNAs) and biomolecules (proteins, RNAs and DNAs) which are experimentally verified" |
2426 |
| TESS |
"TESS is Transcription Element Search System." |
2545 |
| DPVweb |
"This site provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa, with some additional data on animal viruses and phages with RNA or ssDNA genomes. " |
3996 |
| Hollywood |
"Hollywood is a RNA splicing database containing data for the splicing of orthologous genes in different species" |
2467 |
| SARS-Co V RNA SSS |
"SARS-CoV RNA SSS DATABASE is a database of the predicted RNA secondary structural sequences of six SARS coronavirus complete genomes which were sequenced and submitted to GenBank by the separate sequencing and research groups" |
2518 |
| microRNA Registry |
"The miRBase database is a searchable database of published miRNA sequences and annotation representing a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence" |
2456 |
| miRNAMap |
"miRNAMap 2.0 collects experimental verified microRNAs and experimental verified miRNA target genes in human, mouse, rat, and other metazoan genomes. In addition to known miRNA targets, three computational tools previously developed, such as miRanda, RNAhybrid and TargetScan, were applied for identifying miRNA targets in 3' -UTR of genes." |
2513 |
| Plant MPSS |
"Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA." |
2452 |
| NONCODE |
"NONCODE is a database of all kinds of noncoding RNAs (except tRNAs and rRNAs). " |
2344 |
| PLANTncRNAs |
"PLANTncRNAs is a database specially dedicated to plant ncRNAs. This database is not only a repository for known or predicted plant ncRNA sequences, it also includes summaries with prominent characteristics for each gene, such as gene expression and associated mutant phenotypes." |
2445 |
| RNA SSTRAND |
"This database incorporates a comprehensive collection of known RNA secondary structures, and provides the scientific community with ways of analysing, searching and updating the proposed database." |
2669 |
| Rfam |
"Rfam is an open access database, hosted at the Wellcome Trust Sanger Institute, containing information about RNA families." |
2379 |
| SCOR |
"SCOR, the Structural Classification of RNA, is a database designed to provide a comprehensive perspective and understanding of RNA motif three?dimensional structure, function, tertiary interactions and their relationships." |
2436 |
| Argonaute |
"miRWalk is a comprehensive database that provides information on miRNA from Human, Mouse and Rat on their predicted as well as validated binding sites on their target genes. " |
2625 |
| PseudoBase |
"PseudoBase is a database containing structural, functional and sequence data related to RNA pseudo |
2375 |
| snoRNA-LBME-db |
"snoRNA is a database of human C/D box and H/ACA modification guide RNAs" |
2314 |
| HuSiDa |
"HuSiDa is a public database that serves as a depository for both, sequences of published functional siRNA molecules targeting human genes and important technical details of the corresponding gene silencing experiments." |
2344 |
| RNAdb |
"RNAdb is a Comprehensive mammalian noncoding RNA database which contains over 800 unique experimentally studied non-coding RNAs (ncRNAs), including many associated with diseases and/or developmental processes." |
2369 |
| SELEX DB |
"SELEX database accumulates DNA/RNA sequences of sites extracted by means of SELEX-technologies out of the pool of randomized sequences. In addition, SELEX_DB contains computer software for recognition of functional DNA/RNA sites." |
2378 |
|
Top of Page
| Genome Databases |
|
| Site Name |
Description |
Clicks |
| Genomes online database (GOLD |
GOLD "is a World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world". |
2765 |
| NDB |
NDB is a "repository of 3 dimensional structural information about nucleic acids". |
3020 |
| Animal Genome Size Database, Release 2.0 |
Animal Genome Size Database, Release 2.0 is "a comprehensive catalogue of animal genome size data. Haploid DNA contents (C-values, in picograms) are currently available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources". |
3937 |
| A quick guide to sequenced genome |
This Quick Guide to Sequenced Genome "includes descriptions of these organisms and has links to sequencing centers and scientific abstracts". |
3241 |
| Completed genomes: Eukaryotes |
Web resources for completed eukaryotic genomes. |
2655 |
| ArkDB |
"The ArkDB database system aims to provide a comprehensive public repository for genome mapping data from farmed and other animal Species" (viz. cat, deer, chciken, cow, duck, horse, pig, quail etc). It thus targets to "provide a route in to genomic and other sequence from the initial viewpoint of linkage mapping, RH mapping, physical mapping or - possibly more importantly - QTL mapping data". |
2793 |
| The Database of Genomic Variants archive (DGVa) |
The Database of Genomic Variants archive (DGVa) is a repository that provides archiving, accessioning and distribution of publicly available genomic structural variants, in all species. |
3243 |
| Databases for bovine, pig and canine genome |
This website harbors databases for bovine, pig and canine genome as well as information of bovine genome network. |
2619 |
| KEGG |
It’s a “database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies”. |
3593 |
| Karyn's Genomes |
This is a collection and brief description of some of the available sequenced genomes |
2437 |
| Ensembl Genome |
It is genome database maintained by Ensembl for different taxonomic species, viz. Bacteria, Protists, Fungi, Plants, Metazoa and Vertebrates |
3841 |
| CGView Server |
"The CGView Server is a comparative genomics tool for circular genomes (plasmid, bacterial, mitochondrial, and chloroplast) that allows sequence feature information to be visualized in the context of sequence analysis results" |
2763 |
| WormBase (v.WS241) |
"WormBase is an online biological database about the biology and genome of the nematode model organism Caenorhabditis elegans and contains information about other related nematodes" |
4365 |
| Saccharomyces |
"SGD provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relationships between sequence and gene products in fungi and higher organisms" |
2381 |
| EBI Genomes Pages |
"These web pages give access to a large number of complete genomes" |
3481 |
| CoGenT++ |
"CoGenT++ facilitates the re-distribution of all fully sequenced and published genomes, storing information about species, gene names and protein sequences". |
2483 |
| BSORF |
"Bacillus subtilis Genome Database" |
2605 |
| MAPPER |
"The MAPPER database: a multi-genome catalog of putative transcription factor binding sites." |
2452 |
| T4 |
"T4 genome like database provides Genome information about T4-like bacteriophage |
2836 |
| FLAGdb++ |
"FLAGdb++ is dedicated to the integration and visualization of data for high-throughput functional analysis of a fully sequenced genome, as illustrated for Arabidopsis." |
2383 |
| CYGD |
"The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae" |
2415 |
| RsGDB |
"The main role of the R.sphaeroides genome database (RsGDB) is to provide public access to the collected genomic information for R.sphaeroides" |
2406 |
| Human Genome Segmental duplication database |
"The Centre for Applied Genomics (TCAG) is dedicated to conducting and promoting groundbreaking research in genomics including service and training support for academic, government, and private sector scientists worldwide" |
3330 |
| BacMap |
"BacMap is an interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes." |
2643 |
| SGD |
"The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae" |
2650 |
| UCSC Archaeal genome browser |
"The UCSC Archaeal Genome Browser is a window on the biology of more than 100 microbial species from the domain Archaea." |
2423 |
| aPHID |
"This is the aphid genome database that aims to store recently acquired genomic resources on aphids and compares them to other insect resources as functional annotation tools" |
2395 |
| Candida genome |
"Candida Genome Database is a resource for genomic sequence data and gene and protein information for Candida albicans and related species." |
3288 |
| Genolevures |
"Genolevures provides annotated sequence data and classifications for the genomes of eighteen species of hemiascomycete yeasts, including nine complete genomes" |
2399 |
| ShiBase |
"Known and putative virulence factors (or regulation genes) in Shigella genomes" |
2468 |
| NRSub |
"NRSub, a non-redundant database of sequences from this Bacillus subtilis" |
2404 |
| PseudoCAP |
"The Pseudomonas Genome database is a resource for peer-reviewed, continually-updated annotations for the Pseudomonas aeruginosa PAO1 reference strain's genome and comparative analyses of several related Pseudomonas species." |
3445 |
| YGOB |
"YGOB is an online tool for visualising the syntenic context of any gene from several yeast genomes. " |
2936 |
|
Top of Page
| Species specific Databases |
|
| Site Name |
Description |
Clicks |
| BovMap Link |
The site contains links to BovMap database and other genomic resources. |
2810 |
| EcoCyc |
"EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways". |
2673 |
| CMR |
"The Comprehensive Microbial Resource (CMR) is a free website used to display information on all of the publicly available, complete prokaryotic genomes". |
2643 |
| Mouse Genome Informatics |
A very useful site that contains information, data and tools for mouse genome and analytical aspects (viz. gene, SNP, orthology, phenotype and disease model, expression, tumor, function, pathways etc.). |
2605 |
| NAGRP Pig |
This is the website of NAGRP Pig Genome Co-ordination program (USDA, USA). |
2660 |
| Vector DB |
"Vector database is a digital collection of vector backbones assembled from publications and commercially available sources. This is a free resource for the scientific community that is compiled by Addgene. Only the plasmids deposited at Addgene are available for purchase through this website". |
4360 |
| Saccharomyces Genome Database |
"The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relationships between sequence and gene products in fungi and higher organisms". |
3284 |
| Intronless Gene Database |
A highly curated database of eukaryotic intronless genes. |
2646 |
| FlyBase |
It’s "an online bioinformatics database and the primary repository of genetic and molecular data for the insect family Drosophilidae" |
2236 |
| Rat Genome Database |
"The Rat Genome Database is a collaborative effort between leading research institutions involved in rat genetic and genomic research". Its goal is to "to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community". |
2922 |
| BovBASE |
"BovBase is an ACeDB version of the BOVMAP database. BOVMAP is a public database, which contains information on mapped genes and markers in cattle" |
2260 |
| PIGBASE |
PigBase is a genetic database of the domestic swine. |
2254 |
| Mouse Genome Informatics (MGI) |
"MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease" |
2217 |
| MaizeDB |
"MaizeGDB is a community-oriented, long-term, federally funded informatics service to researchers focused on the crop plant and model organism Zea mays" |
3255 |
| ZFIN |
This is the database for the model organism "Zebra Fish" another important model |
4797 |
| DictyBase |
"dictyBase is an online bioinformatics database for the model organism Dictyostelium discoideum." |
3577 |
| MolliGen |
"MolliGen is a database dedicated to the comparative genomics of Mollicutes" |
2379 |
| PROPHECY |
"PROPHECY provides quantitative information about phenotypes for the complete collection of deletion strains in yeast (Saccharomyces cerevisiae)." |
2447 |
| SCMD |
"The Saccharomyces Cerevisiae Morphological Database(SCMD) is a collection of micrographs of budding yeast mutants" |
2209 |
| SCPD |
"SCPD is the The Promoter Database of Saccharomyces cerevisiae" |
2502 |
| Yeast Intron database |
"This site contains information about the spliceosomal introns of the yeast Saccharomyces cerevisiae." |
2515 |
| YEASTRACT |
"YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 206000 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1300 bibliographic references." |
2841 |
| YRC PDR |
"The mission of YRC is to facilitate the identification and characterization of protein complexes in the yeast Saccharomyces cerevisiae." |
2348 |
|
Top of Page
| Specialized Databases |
|
| Site Name |
Description |
Clicks |
| Eukaryotic Promoter Database (EPD) |
EPD is "an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries" |
2922 |
| Organnele Genome DB (GOBASE) |
"GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts. GOBASE is currently expanding to include information on representative bacteria that are thought to be specifically related to the bacterial ancestors of mitochondria and chloroplasts" |
2539 |
| Ribosome Database Project |
This site provides online tools for data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences |
2603 |
| Restriction Enzyme Database (REBASE) |
"REBASE is a database of information about restriction enzymes and DNA methyltransferases. REBASE contains and extensive set of references, sites of recognition and cleavage, sequences and structures" |
2531 |
| TRANSFAC® Transcription Factor Binding Sites |
"TRANSFAC® is a unique knowledge-base containing published data on eukaryotic transcription factors and miRNAs, their experimentally-proven binding sites, and regulated genes. The extensive compilation of binding sites provides the most comprehensive data set of transcription factor–gene interactions available" |
3167 |
| Immunogenetic Database (IMGT/HLA) |
"The IMGT/HLA Database provides a specialist database for sequences of the human major histocompatibility complex (HLA) and includes the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. The IMGT/HLA Database is part of the international ImMunoGeneTics project (IMGT)" |
2603 |
| Proteome Analysis Database |
"It provides access to species descriptions, literature, statistical analysis and summary information about each complete proteome; and integrates data from a variety of sources, including InterPro, CluSTr and GO" |
2277 |
| TRANSFAC |
"TRANSFAC® provides data on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes. TRANSCompel contains data on eukaryotic transcription facotrs experimentally proven to act together in a synergistic or antagonistic manner" |
2837 |
| HIV Sequence Database |
HIVSD provides search interface for retrieving HIV and SIV sequences, tools for alignment and tree building, searching HIV sequences based on geographical distribution, HIV sequence compendium etc. |
2610 |
| International ImMunoGeneTics information system |
IMGT, "the global reference in immunogenetics and immunoinformatics, is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MH superfamily (MhSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates" |
2656 |
| Eukaryotic Gene Orthologues (EGO) |
|
2269 |
| BAli BASE |
"BAliBASE is specifically designed to serve as an evaluation resource to address all the problems encountered when aligning complete sequences. " |
2083 |
| Aptamer database |
"The Aptamer Database is a comprehensive, annotated repository for information about aptamers and in vitro selection. This resource is provided to collect, organize and distribute all the known information regarding aptamer selection." |
2284 |
| CSS |
"CSSdb is a curated collection of great CSS, Sass, LESS and Stylus libraries." |
3399 |
| Cyclonet |
"Cyclonet database - a database on cell cycle regulation in eukaryotes. The database contains information about cell cycle specific genes, proteins, protein complexes and their interactions, diagrams of cell cycle regulation for vertebrates, models of cell cycle and results of their analyses, microarray data, literature references and other related resources" |
2375 |
| EndoNet |
"Endonet is the information resource about the endocrine network in human." |
2181 |
| Kidney Development database |
"The Kidney Development Database was created to collect in one place the data from a large number of developmental studies that have a bearing on the study of kidney development." |
2277 |
| HemBase |
"Hembase is an integrated browser and genome portal designed for web-based examination of the human erythroid transcriptome" |
2278 |
| Mpact |
"This is a database of the confirmed and proposed impact sites and related deposits on the Earth." |
2300 |
| InsulatorDB |
"CTCFBSDB: a CTCF binding site database for characterization of vertebrate genomic insulators. CCCTC-binding factor (CTCF) is a versatile transcription regulator that is evolutionarily conserved from fruit fly to human" |
2256 |
| NCIR |
"A database of prions and other sequences relevant to prion phenomena" |
2180 |
| MAMEP |
"The project is aiming to create a comprehensive information resource for the functional analysis of pattern formation, tissue development and organogenesis. " |
2386 |
| ODB |
"ODB (Operon DataBase) aims to collect known and conserved operons in multiple species. All the known operons are derived from the literature and from publicly available database including operon information" |
2483 |
| GlycoSuiteDB |
"GlycoSuiteDB is a relational database that curates information from the scientific literature on glyco-protein derived glycan structures, their biological sources, the references in which the glycan was described and the methods used to determine the glycan structure" |
2378 |
| TmaDB |
"To analyse TMA output a relational database (known as TmaDB) has been developed to collate all aspects of information relating to TMAs. " |
2307 |
| Monosaccharide browser |
"Monosaccharide Browser allows to view space filling Fischer projections of monosaccharides." |
2229 |
| SuperNatural |
"SuperNatural: a searchable database of available natural compounds" |
2351 |
| CSD |
"The Cambridge Structural Database (CSD), is a repository for small molecule crystal structures. Scientists use single-crystal x-ray crystallography to determine the crystal structure of a compound." |
2668 |
| ChEBI |
"Chebi is the database and ontology of Chemical Entities of Biological Interest" |
2097 |
| Glycan |
"The CFG's Glycan Structures Database offers detailed structural and chemical information for thousands of glycans, including both synthetic glycans and glycans isolated from biological sources" |
2259 |
| IGTC |
"The International Gene Trap Consortium (IGTC) represents all publicly available gene trap cell lines, which are available on a non-collaborative basis for nominal handling fees. " |
2417 |
| CCSD |
"CCSD - Complex Carbohydrate Structure Database (CarbBank)" |
2197 |
| FusionDB |
"FusionDB is a database of bacterial and archaeal gene fusion events - also known as Rosetta stones" |
2147 |
| Lipid MAPS |
"The LIPID MAPS infrastructure is a unique resource for the biomedical community. In addition to providing the largest database of lipid molecular structures, the lipid maps resource contains information on the lipid proteome, quantitative estimates of lipids in the human plasma" |
3974 |
| MethDB |
"MethDB - the database for DNA methylation and environmental epigenetic effects" |
2566 |
| MtDB |
"Human Mitochondrial Genome Database" |
2236 |
| NURSA |
"NURSA is a resource within which bioinformatic and bench research efforts in the field of nuclear receptors can be pursued in a synergistic and multidisciplinary approach, using a common technological platform" |
5486 |
| Path Base |
"Pathbase is a database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. Images can be retrieved by searching for specific lesions or class of lesion, by genetic locus, or by a wide set of parameters shown on the Advanced Search Interface" |
2629 |
| ICDS |
"ICDS database is a database containing ICDS detected by a similarity-based approach". The "Unrecognized frameshifts, in-frame stop codons and sequencing errors lead to Interrupted CoDing Sequence (ICDS) can seriously affect all subsequent steps of functional characterisation, from in silico analysis to high-throughput proteomic projects" |
2220 |
| HIC-Up |
"HIC-Up, the Hetero-compound Information Centre - Uppsala is a freely accessible resource for structural biologists who are dealing dealing with hetero-compounds ("small molecules")." |
2438 |
| NTDB |
"The National Trauma Data Bank |
2639 |
| SWEET-DB |
"This site provides databases and bioinformatics tools for glycobiology and glycomics." |
2115 |
| LifeMap Sciences |
"LifeMap’s Integrated Biomedical Knowledgebase and discovery platform for biomedical research currently includes GeneCards: the leading human gene database; LifeMap Discovery™, the database of embryonic development, stem cell research and regenerative medicine; and MalaCards, the human disease database" |
2627 |
|
Top of Page
| NRSP Databases |
|
| Site Name |
Description |
Clicks |
| Links to AnGR Sites and DB resources |
This site is maintained by National Animal Genome Research Program (NAGRP) (USDA NRSP-8 Livestock Genome Research Projects) and contains an extensive links to various websites and databases for livestock species |
2376 |
| NRSP-8 National Aquaculture Genome Projects |
"The National Aquaculture Genome Project is a part of the National Animal Genome Research Project. This site is designed to enhance collaboration, cooperation, communication, and coordination among aquaculture genome research community members." |
2209 |
| NAGRM Genome Informatics Resources |
This site of NAGRM contains links to Animal genome Data Resources (Map, EST, Bac Contig, HapMap) of several livestock species, Neighbourhood Links (Open Source Tools, DB Tools, Ontology, Fuctional genomics etc), NAGRP Tools resources etc. |
2276 |
| NAGRP Tool Box |
Useful Bioinformatics tools for molecular data analysis, viz. Beap, Categorizer, Cri-Map, SNPlotz etc. |
2068 |
| NAGRP Blast Center |
"A number of BLAST options are available, namely, Regular BLAST, Mega BLAST, BLAST 2 sequences, mpiBLAST". |
2197 |
| NAGRP Cattle Genome Coordination Program |
All required information (through links to main pages) regarding genomics and molecular genetics research on cattle, viz. Research Activities, Databases, Genome Maps, Resources etc. are available in one page. |
2255 |
| NAGRP Cattle genome Maps |
Cattle genome map & QTL maps from various resources are avilable, viz. Cattle Genome Map at NCBI (updated: 2003, 2007), Cattle Genome Map at USDA-MARC (1994, 1996, 2004), Bovine Genome Browser (TXAM Univ), The ArkDB - Cattle Map (Roslin Inst.), Texas A&M, Univ. of Sydney etc. |
2178 |
| AnGenMap |
"ANGENMAP (ANimal GENe MAPpers) is an internet discussion and information sharing group in the broad fields of animal genome research. The purpose of the group is to promote the exchange of information related but not limited to, animal gene mapping, genetics, genomics, and bioinformaitcs" |
2514 |
| Genome research Information Links |
This wesite of NAGRP contains links to various useful areas of bioinformatics andbiological research, viz. Genome Databases, Literature Databases, Livestock Genomics Projects, Gene Prediction Software, Microarray Software and Databases, Genome Computing Resources, Journals in Biology, BioTech Companies and Patent and IP Resources |
2190 |
| AnimalQTLdb |
QTL information on cattle, pig, sheep, horse, chicken, rainbow-trout are avilable. "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) strives to collect all publicly available trait mapping data, i.e. QTL (phenotype/expression, eQTL), candidate gene and association data (GWAS) and copy number variations (CNV) mapped to livestock animal genomes, to facilitate locating and comparing discoveries within and between species. New data and database tools are continually developed to align various trait mapping data to map-based genome features, such as annotated genes". |
7103 |
| Ruminant Genome Biology Consortium |
"The Ruminant Genome Biology Consortium has been formed to capture the learning’s of communities who have already developed genomic tools for their own ruminant (Bovine. Ovine and Caprine) species" |
2128 |
| NAGRP Sheep / Small Ruminants Genome Coordination Program |
All required information (through links to main pages) regarding genomics and molecular genetics research on sheep/small ruminants, viz. Research Activities, Databases, Genome Maps, Resources etc. are available in one page. |
2241 |
| Teleost Alternative Splicing Database |
Alternative splicing information and related databases on catfish, zebrafish, fugu etc are available. |
2143 |
| Spidentifier v. Beta 1.10 |
"This package is designed to predict the location of SNPs from clusters of ESTs produced by the program CAP3" |
2166 |
|
Top of Page
| Genetic Databases |
|
| Site Name |
Description |
Clicks |
| Gene Database |
"The GeneDB project is a core part of the Sanger Institute's Pathogen Genomics activities". It provides "reliable access to the latest sequence data and annotation/curation for the whole range of organisms sequenced by the Pathogen group" and develops "the website and other tools to aid the community in accessing and obtaining the maximum value from these data" |
2340 |
| AceDB |
"AceDB is a database designed specifically for handling genome and bioinformatic data. The tools it provides give great flexibility for the manipulation, display and annotation of genomic data" |
2275 |
| The E. coli Genetic Stock Center |
CGCG is a commercial stock center for non-pathogenic E. coli strains. This center is funded by National Science Foundation. It maintains databases and links to resources on E. coli. |
3759 |
| Links to E.coli db |
Harbors a number of links to various resources of E. coli (by CGSG), viz. Genomic information, protein databases etc. |
2372 |
| AluGene |
"TranspoGene is a publicly available database of Transposed elements (TEs) which are located within protein-coding genes of 7 organisms: human, mouse, chicken, zebrafish, fruilt fly, nematode and sea squirt" |
2275 |
| TPMD |
"TPMD shares useful genotyping information including data of genotyped microsatellite markers, genotyping resources and laboratory supports for promoting genotyping and gene cloning of prevalent diseases." |
2154 |
| NPRD |
"Nucleosome Positioning Region Database (NPRD), which is compiling the available experimental data on locations and characteristics of nucleosome formation sites (NFSs), is the first curated NFS-oriented database. " |
3111 |
| HERVd |
"Human Endogenous Retrovirus Database is compiled from the human genome nucleotide sequences obtained mostly in the Human Genome Projects and makes it possible to continuously improve classification and characterization of retroviral families." |
2755 |
| IDB |
"The NDB contains information about experimentally-determined nucleic acids and complex assemblies." |
2301 |
| Deniz |
"Deniz isan electronic database network for beta-thalassemia allele frequency distributions in the Arab world " |
2222 |
| Genetic Codes |
"This database takes care to ensure that the translation for each coding sequence (CDS) present in GenBank records is correct. Central to this effort is careful checking on the taxonomy of each record and assignment of the correct genetic code" |
3602 |
| MICdb |
"MICAS is an interactive user-friendly web-based analysis server to find non-redundant microsatellites of a selected bacterial or archeal genome sequence." |
2288 |
| CUTG |
"The CUTG database contains a series of codon usage tables calculated from GenBank." |
2392 |
| PEC |
"Shigen stands for shared information of genetic resources and supports the database construction of resources on demand by researchers who maintain genetic resources" |
2495 |
| TRIPLES |
"TRIPLES is a web-accessible database of TRansposon-Insertion Phenotypes, Localization and Expression in Saccharomyces cerevisiae-a relational database housing nearly half a million data points generated from an ongoing study using large-scale transposon mutagenesis to characterize gene function in yeast." |
2246 |
| STRBase |
"Short Tandem Repeat DNA databases are intended to benefit research and application of short tandem repeat DNA markers to human identity testing. |
2107 |
|
Top of Page
| Q-PCR Primer DB |
|
| Site Name |
Description |
Clicks |
| GET-Primer |
This site combines and automates several features critical for optimal qPCR primer design (source: http://openwetware.org/wiki/Choosing_primers_for_qPCR). |
2362 |
| RT Primer DB |
"RTPrimerDB is a public database for primer and probe sequences used in real-time PCR assays employing popular chemistries (SYBR Green I, Taqman, Hybridisation Probes, Molecular Beacon) to prevent time-consuming primer design and experimental optimisation, and to introduce a certain level of uniformity and standardisation among different laboratories". |
2200 |
| PrimerBank |
PrimerBank is a public resource for PCR primers. These primers are designed for gene expression detection or quantification (real-time PCR). PrimerBank contains over 306,800 primers covering most known human and mouse genes. |
4536 |
| qPrimer Depot |
This "database provides qRT PCR primers for 99.96% human RefSeq sequences". |
2289 |
| SYBR Green Primer Sets- QPCR |
"This page provides a link to primer sets that have been synthesized, tested and optimized for the measurement of gene expression in various organisms" |
2193 |
|
Top of Page
| Cancer DB |
|
| Site Name |
Description |
Clicks |
| Atlas of Genetics and cytogenetics in oncology and haemat |
"The Atlas of Genetics and Cytogenetics in Oncology and Haematology is a peer reviewed on-line journal, encyclopaedia and database in free access on the Internet, devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases" |
7328 |
| ITTACA |
"ITTACA(Integrated Tumor Transcriptome Array and Clinical data Analysis)centralizes public datasets containing both gene expression and clinical data and currently focuses on the types of cancer that are of particular interest to the Institut Curie: breast carcinoma, bladder carcinoma, and uveal melanoma" |
2242 |
| Cosmic v68 |
"COSMIC is designed to store and display somatic mutation information and related details and contains information relating to human cancers" |
6391 |
| CGED |
"CGED (Cancer Gene Expression Database) is a database of gene expression profile and accompanying clinical information" |
2215 |
| IARC TP53 database |
"The IARC TP53 Database compiles various types of data and information on human TP53 gene variations related to cancer." |
2946 |
| SNP500Cancer |
"SNP cancer500 web site serves as the public portal to our genotyping data and analysis results generated by Next-Gen sequencing" |
6061 |
| MTB |
"The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer." |
2289 |
| RTCGD |
"Retroviral tagged cancer gene database manages multiple high?throughput insertional mutagenesis screening projects." |
2289 |
| Database of |
"The database describes each p53 mutation (type of the mutation, exon and codon affected by the mutation, nucleotide and amino acid change), each family (family history of cancer, diagnosis of Li-Fraumeni syndrome), each affected individual (sex, generation, p53 status, from which parent the mutation was inherited) and each tumour (type, age of onset, p53 status |
2204 |
| Tumor Gene family databases |
"The Tumor Gene Family of Databases contains information about genes which are targets for cancer-causing mutations; proto-oncogenes and tumor supressor genes." |
2080 |
| Oral Cancer Gene database |
"The Tumor Gene Family of Databases contains information about genes which are targets for cancer-causing mutations; proto-oncogenes and tumor supressor genes." |
2189 |
| Oncomine |
To study the overexpression of tumor types this site can be used. Microarray and other data on tumors are available here. |
3599 |
| Cancer Chromosomes |
This site can be used to "search for comprehensive Cytogenetic, clinical, and reference information on cancer-related aberrations" |
2155 |
|
Top of Page
| Chromosome Databases |
|
| Site Name |
Description |
Clicks |
| GeneLoc |
"GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm" |
2316 |
| IXDB |
"The Integrated X Chromosome Database (IXDB is a repository for physical mapping data of the human X chromosome and aims at providing a global view of genomic data at a chromosomal level" |
2079 |
| NCBI Map Viewer |
"The Map Viewer provides a wide variety of genome mapping and sequencing data" |
2513 |
| SKY/M-FISH and CGH |
"The goal of the SKY/M-FISH and CGH database is to provide a public platform for investigators to share and compare their molecular cytogenetic data. The database is open to veryone and all users can view an individual investigator's public data or compare public cases from different investigators" |
2143 |
|
Top of Page
| Coexpression & Pathway DB |
|
| Site Name |
Description |
Clicks |
| Biozon |
"Biozon is a unified biological resource on DNA sequences, proteins, complexes and cellular pathways." |
2079 |
| CopS |
"CoP is a database for characterizing co-expressed gene modules with biological information in plants." |
2066 |
| BioSilico |
"BioSilico is a web-based database system that facilitates the search and analysis of metabolic pathways." |
2276 |
| PathDB |
"ConsensusPathDB-human integrates interaction networks in Homo sapiens including binary and complex protein-protein, genetic, metabolic, signaling, gene regulatory and drug-target interactions, as well as biochemical pathways." |
2793 |
| TRANSPATH |
"TRANSPATH |
2071 |
| ROSPath |
"Reactive oxygen species (ROS) signaling pathway proteins" |
2105 |
| aMAZE |
"AMAZE: a database of molecular function, interactions and biochemical processes" |
2188 |
| STCDB |
"The Signal Transduction Classification Database (STCDB) is a database of information relative to the classification of signal transduction." |
2106 |
| BioCarta |
"Biocarta is a commercial company which provides a wide array of organic and biochemical products. Their website contains a large database of pathways in organisms as well. Pathways are given in graphical representations supported by explaining text." |
2107 |
| BioCyc |
"BioCyc is a collection of 3530 Pathway/Genome Databases (PGDBs), with tools for understanding their data." |
3233 |
| BRITE |
"KEGG BRITE is a collection of manually created hierarchical text (htext) files capturing functional hierarchies of various biological objects, especially those represented as KEGG objects" |
3889 |
| MetaCyc |
"MetaCyc is a database of experimentally elucidated metabolic pathways from all domains of life." |
2131 |
| Reactome |
"Reactome is a free, open-source, curated and peer reviewed pathway database that provides intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology and education." |
3146 |
| GeneNet |
"The GeneNet system is designed for formalized description and automated visualization of gene networks." |
2246 |
|
Top of Page
| Disease Related DB |
|
| Site Name |
Description |
Clicks |
| CTGA |
"Catalogue for Transmission Genetics in Arabs" (CTGA) is a database for genetic disorders in Arab populations that hosts entries for nearly 1580 Mendelian disorders and related genes." |
2519 |
| PROMISE |
"ProMISe (Project Manager Internet Server) is a web based relational database management system for the design, maintenance and use of (clinical) data management. " |
2423 |
|
Top of Page
| Enzyme Databases |
|
| Site Name |
Description |
Clicks |
| TCDB |
"The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system which is analogous to the Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information." |
3550 |
| PRECISE |
"PRECISE (Predicted and Consensus Interaction Sites in Enzymes) is a database of interactions between the amino acid residues of an enzyme and its various ligands, i.e., substrate and transition state analogues, cofactors, inhibitors, and products." |
2188 |
| TECRdb |
"TECRdb is a database for thermodynamics of enzyme-catalyzed reactions" |
2159 |
| CSA |
"The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. " |
2216 |
|
Top of Page
| EST DB |
|
| Site Name |
Description |
Clicks |
| DiArk |
"diArk is a database driven web application that is designed to store, organize, and present the most relevant information about completed genome projects and EST/cDNA data from eukaryotes" |
2319 |
| GeneNest |
"GeneNest is a comprehensive visualization of gene indices of the following organisms. The aim of GeneNest is to represent each gene by a single cluster of ESTs and/or mRNAs" |
2074 |
| TIGR Gene Indices |
"The TIGR Gene Indices are a collection of species-specific databases that use a highly refined protocol to analyze EST sequences in an attempt to identify the genes represented by that data and to provide additional information regarding those genes." |
1887 |
| CryptoDB |
"The database, CryptoDB is a community bioinformatics resource for the AIDS-related apicomplexan-parasite, Cryptosporidium. CryptoDB integrates whole genome sequence and annotation with expressed sequence tag and genome survey sequence data and provides supplemental bioinformatics analyses and data-mining tools." |
2958 |
| EASED |
"The Extended Alternatively Spliced EST Database is an online compendium of ASforms for several organisms. ASforms are defined by comparing high?scoring ESTs with mRNA sequences using BLAST, taking known exon |
2096 |
| EDAS |
"EDAS (EST Derived Alternative Splicing Database) is a database of alternative splicing derived from the anlaysis of genomic, protein, mRNA and EST data." |
2023 |
| GeneTide |
"GeneTide is an automated system for human transcripts (mRNA & ESTs) annotation and elucidation of de-novo genes." |
2058 |
| ChimerDB |
"ChimerDB is the database of fusion sequences encompassing bioinformatics analysis of mRNA and EST sequences in the GenBank, manual collection of literature data, and integration with other known database such as OMIM." |
2147 |
| TBestDB |
"The taxonomically broad EST database TBestDB serves as a repository for EST data from a wide range of eukaryotes, many of which have previously not been thoroughly investigated. " |
2122 |
| ApiEST-DB |
"APIest database provides integrated access to publicly available EST data from protozoan parasites in the phylum Apicomplexa. " |
1965 |
| openSputnik |
"Over four million ESTs from over 50 distinct plant species have been collated within an EST analysis pipeline called openSputnik. These have been annotated using orthology-based annotation transfer from reference plant genomes and using a variety of contemporary bioinformatics methods to assign peptide, structural and functional attributes." |
2103 |
| LumbriBASE |
"The Lumbricus rubellus genome project and annelid EST database" |
2439 |
|
Top of Page
| Exon-Intron & Splicing DB |
|
| Site Name |
Description |
Clicks |
| ASAP |
"ASAP access and mine alternative splicing information coming from genomics and proteomics based on genome-wide analyses of alternative splicing in human (30 793 alternative splice relationships found) from detailed alignment of expressed sequences onto the genomic sequence." |
2126 |
| EID |
"The Exon-Intron Database (EID) is a flat-file, Fasta-formated collection of sequences and annotations for all exons and introns obtained from GenBank. " |
2334 |
| ExInt |
"The Exon/Intron Database (ExInt) stores information of all GenBank eukaryotic entries containing an annotated intron sequence" |
2194 |
| UTRdb/UTRsite |
"UTRSite is a collection of functional sequence patterns located in 5' or 3' UTR sequences." |
2100 |
| Intronerator |
"The Intronerator is a database of alternatively spliced genes and a database of introns for Caenorhabditis elegans" |
2076 |
| ASDB |
"ASDB (Alternative Splicing Data Base) contains 1922 protein and 2486 DNA sequences. The protein entries from SWISS-PROT are joined into clusters corresponding to alternatively spliced variants of one gene. The DNA division consists of complete genes with alternative splicing mentioned or annotated in GenBank." |
1966 |
| SpliceDB |
"SpliceDB is a database of canonical and non-canonical mammalian splice sites" |
2092 |
| SpliceInfo |
"Spliceinfo is an information repository for mRNA alternative splicing in human genome " |
2064 |
| SpliceNest |
"SpliceNest is a public database with a web-based, interactive graphical user interface." |
2126 |
| HS3D |
"HS3D (Homo Sapiens Splice Sites Dataset) is a data set of Homo Sapiens Exon, Intron and Splice regions extracted from GenBank Rel.123.The aim of this data set is to give standardized material to train and to assess the prediction accuracy of computational approaches for gene identification and characterization." |
2011 |
|
Top of Page
| Gene & Element Databases |
|
| Site Name |
Description |
Clicks |
| HGT-DB |
"The Horizontal Gene Transfer DataBase (HGT-DB) is a genomic database that includes statistical parameters such as G+C content, codon and amino-acid usage, as well as information about which genes deviate in these parameters for prokaryotic complete genomes" |
1944 |
| Coding DNA ACLAME |
"ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons." |
2510 |
| HemoPDB |
"he Hematopoiesis Promoter Database (HemoPDB) has been developed as a publicly available, web-based information resource focused on transcriptional regulation in hematopoiesis. HemoPDB is composed of integral, experimentally defined regulatory information, including TFs, cis-regulatory elements, their target gene promoters and corresponding annotations, with links to supporting published references." |
2162 |
| \RED |
"ARED searches for AREs (AU-rich elements) in the introns of human genes raising the full repertoire of the ARE-regulome to at least 50% of human protein coding genes." |
2126 |
| DG-CST |
"The DG-CST database is a collection of conserved sequence elements, identified by a systematic genomic sequence comparison between a set of human genes involved in the pathogenesis of genetic disorders and their murine counterparts" |
2188 |
| GenAtlas |
It provides "the international scientific and medical community with scientific and clinical digests on genes and diseases" |
2279 |
| LlBase |
"L1Base is a dedicated database containing putatively active LINE-1 (L1) insertions residing in human and rodent genomes: a) intact in the two ORFs, full length L1s (FLI-L1s) and b) L1s with intact ORF2 but disrupted ORF1 (ORF2-L1s)" |
2147 |
| MGC |
"The goal of the Mammalian Gene Collection (MGC), a trans-NIH initiative, is to provide researchers with unrestricted access to sequence-validated full-length protein-coding (FL-CDS) cDNA clones for human, mouse, and rat genes" |
2329 |
| ORFDB |
Its an ORF browser provided by Lifetechnologies |
2132 |
| Hoppsigen |
"Hoppsigen is a nucleic database of homologous processed pseudogenes (retroelements like SINE and LINE)." |
2028 |
| SOURCE |
"SOURCE is a unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into easy to navigate GeneReports" |
2004 |
| Diatom EST database |
"The Diatom EST database provides integrated access to expressed sequence tag (EST) data from two eukaryotic microalgae of the class Bacillariophyceae, Phaeodactylum tricornutum and Thalassiosira pseudonana." |
2032 |
| Mobile group II introns |
"The database for mobile group II introns provide correct information on the introns, particularly in bacteria including information on introductory information on group II introns; detailed information on subfamilies of intron RNA structures and intron-encoded proteins; a listing of identified introns with correct boundaries, RNA secondary structures and other detailed information; and phylogenetic and evolutionary information." |
2078 |
| HumHot |
"HUMHOT is a web based database of human meiotic recombination hot spot DNA sequences. The database includes the hot spot sequences (<4 kb) obtained from published literature describing the high resolution mapping of human meiotic hot spots and also the hot spot flanking sequence information." |
2168 |
|
Top of Page
| Gene Expression Db |
|
| Site Name |
Description |
Clicks |
| UniGene |
"UniGene computationally identifies transcripts from the same locus; analyzes expression by tissue, age, and health status; and reports related proteins (protEST) and clone resources" |
2235 |
| EICO DB |
"EICO DB is an integrated database for discovery of novel imprinted genes. EICO DB provides candidate imprinted genes by cDNA microarray and single Nucleotide Polymorphisms between MSM and C57BL/6J within RIKEN mouse full-lenght cDNA for validation of imprinting." |
2037 |
| 5'SAGE |
"To comprehensively identify transcription start sites and the frequencies of individual mRNAs in human cell libraries, a method of 5' end Serial Analysis of Gene Expression (SAGE) was developed which makes it possible to collect a large amount of start site information, and subsequently" |
2171 |
| AGD |
"AGD 3.0 is a genome/transcriptome database containing gene annotation and high-density oligonucleotide microarray expression data for protein-coding genes from Ashbya gossypii and the model organism Saccharomyces cerevisiae" |
2193 |
| MEPD |
"The Medaka Expression Pattern Database (MEPD) stores and integrates information of gene expression during embryonic development of the small freshwater fish Medaka (Oryzias latipes)." |
2066 |
| Tooth Development database |
"This site is for the study of gene expression in tooth" |
2396 |
| CAGE |
"Cap-analysis gene expression (CAGE) Basic and Analysis Databases store an original resource produced by CAGE, which measures expression levels of transcription starting sites by sequencing large amounts of transcript 5? ends, termed CAGE tags. " |
2325 |
| FlyView |
"FlyView is the beginning of an image database on Drosophila development and genetics, especially on expression patterns of genes (enhancer trap lines, cloned genes).The concept of FlyView includes compatibility to FlyBase, the main Drosophila database. " |
2197 |
| GeneNote |
"GeneNote is a database of gene expression in normal adult human tissues, based on in-house DNA array experiments using Affymetrix GeneChip HG-U95A-E" |
2125 |
| GeneAnnot |
"GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and
HG-U133 Plus2.0. Probe-sets are related to GeneCards genes, by direct sequence comparison of probes to GenBank, RefSeq and Ensembl mRNA sequences, while assigning sensitivity and specificity scores to each probe-set to gene match. The results are integrated with the GeneCards, GeneLoc and GeneNote databases." |
2183 |
| ECgene |
"EC gene provide functional annotation for alternatively spliced genes. The applications encompass the genome-based transcript modeling for alternative splicing (AS), domain analysis with Gene Ontology (GO) annotation and expression analysis based on the EST and SAGE data." |
2091 |
| GPX |
"GPX macrophage expression atlas is a database for expression profiles of macrophages challenged with a a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults." |
2098 |
| Arabidopsis MPSS |
"Arabidopsis MPSS is an Online Resource for Quantitative Expression Analysis. It is a public, Web-based resource for the analysis of gene expression in the model plant, Arabidopsis. " |
2077 |
| MtbRegList |
"A database dedicated to the analysis of gene expression and regulation data in Mycobacterium tuberculosis. " |
2144 |
| PRODORIC |
"PRODORIC |
2007 |
| Stanford microarray database |
"The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data." |
2326 |
| GermOnline |
"GermOnline provides information and microarray expression data for genes involved ... and array data visualization," |
2241 |
| RefExA |
"SBM DB is comprehensive database of Gene Expression Profiles, which enable to compare the transcriptome of various tissues, organs and experiments." |
2041 |
| GEO |
"GEO is a public functional genomics data repository supporting MIAME-compliant data submissions" |
2756 |
| RECODE |
"Recode2 is a database of genes that utilize non-standard translation for gene expression purposes" |
2049 |
| NetAffx |
"Affymetrix develops and provides innovative technologies that enable multiplex and parallel analysis of biological systems at the cell, protein, and gene level, facilitating the rapid translation of results into biology for a better world." |
2785 |
| rOGED |
"rOGED is rat ovarian gene expression database" |
1978 |
| AOBase |
"Antisense oligonucleotides (ODNs) technology is one of the important approaches for the sequence-specific knockdown of gene expression." |
2217 |
| EPConDB |
"EPConDB is a public web site that supports research in diabetes, pancreatic development and beta-cell function by providing information about genes expressed in cells of the pancreas." |
2004 |
| EpoDB |
"EpoDB( Erythropoiesis database) is a database of genes that relate to vertebrate red blood cells. It includes DNA sequence, structural features, protein information, gene expression information and transcription factor binding sites." |
2002 |
| CisRed |
"The cisRED database holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations." |
2307 |
| Clean Ex |
"CleanEx is a database which provides access to public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-dataset comparisons." |
2214 |
| Axeldb |
"Axeldb is a database storing and integrating gene expression patterns and DNA sequences identified in a large-scale in situ hybridization study in Xenopus laevis embryos." |
2175 |
| ArrayExpress |
"ArrayExpress is a core EBI database delivered by the Functional Genomics group. The database is a repository for functional genomics data from both microarray and high-throughput sequencing studies" |
3429 |
| EMAGE |
"EMAGE is a database of in situ gene expression data in the mouse embryo and an accompanying suite of tools to search and analyse the data." |
2625 |
| emap Atlas |
"The e-Mouse Atlas Project that is a combines resource projects and Resources provided by EMAP are the EMA Anatomy Atlas of Mouse Development and the EMAGE Gene Expression Database." |
1969 |
| GenePaint |
"GenePaint.org is a digital atlas of gene expression patterns in the mouse." |
2013 |
| MAGEST |
"MAGEST is a database of maternal gene expression information for an Ascidian, Halocynthia roretzi. The ascidian has become an animal model in developmental biological research because it shows the simple developmental process and belongs to the one of chordate groups." |
2037 |
| GENSAT |
"GENSAT is an NIH-funded , publicly available gene expression atlas of the developing and adultcentral nervous system in the mouse" |
2596 |
| H-ANGEL |
"The Human Anatomic Gene Expression Library (H-ANGEL) is a resource for information concerning the anatomical distribution and expression of human gene transcripts." |
2091 |
| GXD |
"The Gene Expression Database (GXD) is a community resource for gene expression information from the laboratory mouse. GXD stores and integrates different types of expression data and makes these data freely available in formats appropriate for comprehensive analysis." |
3835 |
| LOLA |
"List Of Lists Annotated (LOLA) is a web driven database of published and manually curated (public), and user-specific (private) gene lists derived from genome-wide approaches such as expression profiling and proteomics." |
2058 |
| BodyMap |
"The microRNA body map is a repository of RT-qPCR miRNA expression data and functional miRNA annotation in normal and diseased human tissues" |
2020 |
| SAGEmap |
"Seial analysis of gene expression (SAGE)is a public gene expression resource and the SAGE libraries are accessioned through geo repository" |
2031 |
| Osteo-promoter database |
"The Osteo-Promoter Database (OPD) is a collection of genes and promoters expressed in skeletal cells." |
2035 |
| PEDB |
"The Prostate Expression Database (PEDB) is a curated relational database and suite of analysis tools designed for the study of prostate gene expression in normal and disease states." |
1972 |
| PEPR |
"The primary goal of PEPR is to determine if the larger scientific community can be given simple, intuitive, and user-friendly web-based access to large microarray data sets. " |
2062 |
| BarleyBase |
"PLEXdb is committed to making expression data publicly available to researchers world-wide" |
2105 |
| BGED |
"Brain Gene Expression Database (BGED) contains gene expression data for various physiological and pathological processes in mouse brain." |
3694 |
| SIEGE |
"The SIEGE database is a clinical resource for compiling and analyzing gene expression data from epithelial cells of the human intra-thoracic airway." |
2154 |
| Mouse SAGE |
"Serial analysis of gene expression (SAGE) is a powerful tool that allows the analysis of overall gene expression patterns with digital analysis." |
1992 |
| yMGV |
"The Yeast Microarray Global Viewer (yMGV) is an on-line database providing a synthetic view of the transcriptional expression profiles of yeast genes among most of the published expression datasets." |
2275 |
| HugeIndex |
"Human Gene Expression Index (HuGE Index) aims to provide a comprehensive database to aid in understanding the expression of human genes in normal human tissues." |
2116 |
| BodyMap-Xs |
"BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression." |
2108 |
| DRASTIC |
"Database Resource for the Analysis of Signal Transduction in Cells (DRASTIC) is a manually derived database of plant expressed sequence tags and genes up- or down-regulated in response to various pathogens, chemical treatments, and abiotic stress such as drought, salt and cold." |
1923 |
|
Top of Page
| HIV Database |
|
| Site Name |
Description |
Clicks |
| HIV Sequence database |
"The HIV databases contain data on HIV genetic sequences, immunological epitopes, drug resistance-associated mutations, and vaccine trials. " |
2350 |
| HIV Drug Resistance database |
"A curated public database designed to represent, store and analyse the divergent forms of data underlying HIV resistance" |
2917 |
| HIV R T and sequence database |
"A curated public database designed to represent, store and analyse the divergent forms of data underlying HIV resistance" |
2330 |
| HIV Molecular immunology database |
"The HIV Molecular Immunology Database is an annotated, searchable collection of HIV-1 cytotoxic and helper T-cell epitopes and antibody binding sites." |
2235 |
|
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