| Immunogenetics DB |
|
| Site Name |
Description |
Clicks |
| IPD |
"The Immuno Polymorphism Database (IPD) provides a centralised system for the study of polymorphism in genes of the immune system." |
2388 |
| Interferon Stimulated gene database |
"This database is an upgrade of the original database and contains type I, II and III interferon (IFN) regulated genes, manually curated from publicly available microarray datasets." |
5271 |
| IL2Rgbase |
"A database of gamma c-chain defects causing human X-linked severe combined immunodeficiency. " |
2635 |
| FIMM |
"FIMM database contains data relevant to functional molecular immunology, focusing on cellular immunology." |
2635 |
| MHCPEP |
"MHCPEP is a curated database comprising over 4000 peptide sequences known to bind MHC molecules." |
2410 |
| HLA Ligandj motif |
"HLA ligand database provides scientists and clinicians with access to Major Histocompatibility Complex (MHC) class I and II motif and ligand data." |
2413 |
| IPD-ESTDAB |
"ESTDAB aims to provide a service enabling investigators to search on-line for HLA-typed, immunologically-characterised tumour cells available for distribution from a central bank." |
2496 |
| IMGTjHLA |
"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." |
3396 |
| IPD-KIR |
"The database provides a centralised repository for human KIR sequences. Killer-cell Immunoglobulin-like Receptors (KIR) have been shown to be highly polymorphic at the allelic and haplotypic level." |
3253 |
| IMGT |
"IMGT®, the international ImMunoGeneTics information system, is the global reference in immunogenetics and immunoinformatics" |
2668 |
| IMGTjGene-DB |
"IMGT/GENE-DB allows a search per gene name and is based on the CLASSIFICATION concept of IMGT-ONTOLOGY" |
2354 |
| IMGT/LIGM-DB |
"IMGT/LIGM-DB is the first database of IMGT®, the international ImMunoGeneTics information system®, the high-quality integrated database specializing in Immunoglobulins (IG), T cell Receptors (TR) and Major Histocompatibility Complex (MHC) molecules of all vertebrate species" |
2543 |
| IMGT/ |
"IMGT® 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. IMGT® provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules" |
2484 |
| MHCBN |
"The MHCBN is a curated database consisting of detailed information about Major Histocompatibility Complex (MHC) Binding,Non-binding peptides and T-cell epitopes" |
2370 |
| JenPep |
"JenPep is a family of relational databases supporting the growing community of immunoinformaticians. It contains quantitative data on peptide binding to Major Histocompatibility Complexes (MHCs) and to Transmembrane Peptide Transporter (TAP), as well as an annotated list of T-cell epitopes." |
2174 |
| dbMHC |
"The dbMHC database provides an open, publicly accessible platform for DNA and clinical data related to the human Major Histocompatibility Complex (MHC)." |
2475 |
| VBASE2 |
"VBASE2 is an integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. All variable gene sequences are extracted from the EMBL-Bank." |
2865 |
| IPD-MHC |
"The IPD-MHC Database provides a centralised repository for sequences of the Major Histocompatibility Complex (MHC) from a number of different species. " |
3329 |
| BCIpep |
"Bcipep is a database of experimentally determined linear B-cell epitopes of varying immunogenicity" |
2222 |
|
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| Mol. Interaction DB |
|
| Site Name |
Description |
Clicks |
| PINT |
"The first release of Protein-protein Interactions Thermodynamic Database (PINT) contains >1500 data of several thermodynamic parameters along with sequence and structural information, experimental conditions and literature information." |
2396 |
| hp-DPI |
"hp-DPI is a protein interaction database for validation of two-hybrid assays of Helicobacter pylori, and prediction of putative protein interactions not yet discovered experimentally." |
2238 |
| 3DID |
"The database of three-dimensional interacting domains (3did) is a collection of high-resolution three-dimensional structural templates for domain-domain interactions. It contains templates for interactions between two globular domains as well as novel domain-peptide interactions" |
2854 |
| PDZBase |
"PDZBase is a manually curated protein-protein interaction database developed specifically for interactions involving PDZ domains" |
2328 |
| MPID |
"The MHC-Peptide Interaction Database-TR version 2 (MPID-T2) is a new generation database for sequence-structure-function information on T cell receptor/peptide/MHC interactions. It contains all known crystal structures of TR/pMHC and pMHC complexes, with emphasis on the structural characterization of these complexes." |
2457 |
| AANT |
"Amino Acid-Nucleotide Interaction Database categorizes all amino acid-nucleotide interactions from experimentally determined protein-nucleic acid structures, and provides users with a graphic interface for visualizing these interactions in aggregate." |
2483 |
| DIP |
"The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions." |
2581 |
| Inter-chain beta sheets |
"A database of protein-protein interactions mediated by interchain ß-sheet formation" |
2402 |
| PINdb |
"Proteins Interacting in the Nucleus database (PINdb) is a database of protein complexes purified from the nucleus of human and yeast cells." |
2314 |
| PSIbase |
"PSIbase is a molecular interaction database that focuses on structural interaction of proteins and their domains, is based on PSIMAP that is a map of protein interactome and covers the interaction of all known 3D protein structures. " |
2358 |
| STRING |
"STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations" |
2285 |
| BioGrid |
"BioGRID (the Biological General Repository for Interaction Datasets) is an online interaction repository with data compiled through comprehensive curation efforts" |
4786 |
| HPID |
"HPID allows the user to use the protein IDs in ENSEMBL, HPRD and UniProt/Swiss-Prot ID to search protein interactions of interest." |
2259 |
| ProNIT |
"ProNIT database provides experimentally determined thermodynamic interaction data between proteins and nucleic acids" |
2336 |
| KDBI |
"Kinetic Data of Bio-molecular Interactions (KDBI) aimed at providing experimentally determined kinetic data of protein-protein, protein-RNA, protein-DNA, protein-ligand, RNA-ligand, DNA-ligand binding or reaction events described in the literature." |
2343 |
| DDIB |
"The Database of Domain Interactions and Bindings (DDIB) collects information about domain-domain interactions and domain interactions with biological molecules such as nucleotides, peptides, inorganic ions, phospholipids." |
2317 |
| IntAct project |
"IntAct provides a freely available, open source database system and analysis tools for molecular interaction data." |
2894 |
| Epitome |
"Epitome is a database of all known antigenic residues and the antibodies that interact with them, including a detailed description of residues involved in the interaction and their sequence / structure environments." |
2803 |
|
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| Mutation Database |
|
| Site Name |
Description |
Clicks |
| Imprinted Gene Catalogue |
"The database includes descriptions of 85 imprinted genes from several mammalian species, over 300 entries on reported parent-of-origin effects in animals, and 1700 mutations (found in 59 different genes) with a parent-of-origin effect. Data is accessed through a search engine and references are hyperlinked to PubMed, UCSC Genome Browser and Ensembl." |
2469 |
| 16Sand 23S rRNA Mutation Database |
"Expanded versions of the 16S and 23S Ribosomal RNA Mutation Databases" |
2233 |
| HGMD |
"The Human Gene Mutation Database (HGMD®) represents an attempt to collate known (published) gene lesions responsible for human inherited disease." |
2313 |
| BayGenomics |
"The BayGenomics gene-trap resource provides researchers with access to thousands of mouse embryonic stem (ES) cell lines harboring characterized insertional mutations in both known and novel genes." |
2229 |
| GeneTrap |
"Gene trapping is a high-throughput approach that is used to introduce insertional mutations across the genome in mouse embryonic stem (ES) cells. In addition to generating standard loss-of-function alleles, newer gene trap vectors offer a variety of post-insertional modification strategies for the generation of other experimental alleles. " |
2545 |
| Cypriot National mutation Database |
"Cypriot National Genetic Database is an online repository of information about inherited disorders in the Cypriot population." |
2271 |
| RBI Gene mutation database |
"RB1 Gene Mutation DB is a locus specific database that contains data on small mutations in RBI gene somatic and germline mutations." |
2331 |
| SSU rRNA modification database |
"The Small Subunit rRNA Modification Database provides a listing of reported post-transcriptionally modified nucleosides and sequence sites in small subunit rRNAs from bacteria, archaea and eukarya." |
2210 |
|
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| Parasite Database |
|
| Site Name |
Description |
Clicks |
| Full-Malaria |
"FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum" |
2266 |
| CandidaDB |
"A new multi-genome GenoList browser is available which includes the genomes of Candida albicans and other Candida species. " |
2278 |
| TcruziDB |
"TcruziDB is an integrated genome database for the parasitic organism Trypanosoma cruzi, the causative agent of Chagas' disease. " |
2507 |
| ToxoDB |
"ToxoDB is a genome and functional genomic database for the protozoan parasite Toxoplasma gondii. " |
2620 |
| PlasmoDB |
"PlasmoDB is a genomic database for the genus Plasmodium." |
5048 |
|
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| Phylogenetic Database |
|
| Site Name |
Description |
Clicks |
| HOINVGEN release 01 |
"HOINVGEN is a database of homologous invertebrate genes, structured under ACNUC sequence database management system. It allows one to select sets of homologous genes among invertebrate species, and to visualize multiple alignments and phylogenetic trees" |
2363 |
| Islander |
"Focuses on integrase phylogeny and helps understand how new site-specificity evolves, an important problem in genome evolution. Prokaryotic chromosomes often contain islands (prophages, pathogenicity islands, etc.) that were delivered by site-specific integrases. Most often the integration sites are in genes for tRNAs or other small RNAs." |
2283 |
| SRPDB |
"SRPDB (Signal Recognition Particle Database) provides aligned, annotated and phylogenetically ordered sequences related to structure and function of SRP. " |
2283 |
| Tree of Life |
"The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. " |
2159 |
| TreeBase |
"TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa" |
3368 |
| DART |
"The DART (Discovery and Aggregation of Relations in Text) database contains approximately 23 million distinct "world knowledge" propositions (110 million with duplicates), extracted from text by abstracting parse trees. " |
2219 |
| PANDIT |
"Protein and Associated Nucleotide Domains with Inferred Trees" |
2895 |
| NeBI Taxonomy |
"The Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases" |
2500 |
| PALl |
"The database of Phylogeny and ALIgnment of homologous protein structures (PALI) contains structure-based sequence alignments and dendrograms based on information primarily derived from the structural alignments at domain level" |
2096 |
| U-genome |
"This database is of importance in understanding unicellular genome design and architecture and evolution related studies." |
2198 |
|
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| Plant Bioinfo. DB |
|
| Site Name |
Description |
Clicks |
| PLACE |
"PLACE is a database of motifs found in plant cis-acting regulatory DNA elements, all from previously published reports." |
2147 |
| PlantCARE |
"PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors." |
2200 |
| AGRIS |
"AGRIS (International System for Agricultural Science and Technology) is a global public domain database with more than 4 million structured bibliographical records on agricultural science and technology." |
2167 |
| ARAMEMNON |
"A specialized database (DB) for Arabidopsis membrane proteins, ARAMEMNON, was designed that facilitates the interpretation of gene and protein sequence data by integrating features that are presently only available from individual sources." |
2337 |
| Arabidopsis Nucleolar |
"The Arabidopsis Nucleolar Protein Database provides information on 217 proteins identified in a proteomic analysis of nucleoli isolated from Arabidopsis cell culture. " |
2139 |
| SGMD |
"It serves both as a sequence repository, holding DNA sequences for numerous EST's, and also as a microarray experiment database. It allows scientists to explore the expression levels of the EST clones stored in the database and to correlate expression levels with function." |
2216 |
| Rice PIPELINE |
"The Rice PIPELINE is a unification tool for plant functional genomics." |
2261 |
| DATF |
"The Database of Arabidopsis Transcription Factors (DATF) collects all arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families." |
2326 |
| GabiPD |
"GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. " |
2203 |
| PoMaMo |
"This is the database for potato maps and more" |
2218 |
| Rice Proteome Database |
"The information thus obtained from the rice proteome will be helpful in predicting the function of the unknown proteins and aid in their molecular cloning." |
2151 |
| Brassica ASTRA |
"Brassica ASTRA is a public database for genomic information on Brassica species. The database incorporates expressed sequences with Swiss-Prot and GenBank comparative sequence annotation as well as secondary Gene Ontology (GO) annotation derived from the comparison with Arabidopsis TAIR GO annotations." |
2425 |
| PlantProm |
"PlantProm DB, a plant promoter database, is an annotated, non-redundant collection of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start site(s), TSS, from various plant species." |
2437 |
| TIGR Maize Database |
"TIGR maize database" |
2301 |
| MOsDB |
"The MOsDB is a resource for publicly available sequences of the rice (Oryza sativa L.) genome" |
2396 |
| ARTADEdb |
"ARTADE (ARabidopsis Tiling-Array-based Detection of Exons) is a standard tool for the annotation of genome-wide tiling-array data in Arabidopsis." |
2111 |
| OryGenesDB |
"The aim of this Oryza sativa database is to display sequence information resulting from the activities of our group, such as the T-DNA and Ds flanking sequence tags (FSTs) produced in the framework of the French genomics initiative Genoplante and the EU consortium Cereal Gene Tags. " |
2604 |
| Oryza Tag Line Data- |
"Oryza Tag Line consists in a searchable database integrating phenotypic data resulting from the evaluation of the G |
2655 |
| PLANT-PIs |
"PlantPIs is a web querying system for a database collecting plant protease inhibitors data" |
2237 |
| PlantsP/PlantsT |
"The PLANTS Database provides standardized information about the vascular plants, mosses, liverworts, hornworts, and lichens of the U.S. and its territories." |
2229 |
| RARGE |
" To enhance the utility of the RIKEN Arabidopsis resource (full-length cDNAs, transposon mutants and microarray experiments), RARGE database was constructed. In order to facilitate effectively phenomics studies, the area of data was integrated from genome to phenome such as Ds tagged mutant and nuclear-encoded chloroplast proteins." |
2284 |
| BGI-RISe |
"In BGI-RIS, sequence contigs of Beijing indica and Syngenta japonica have been further assembled and anchored onto the rice chromosomes. " |
2218 |
| RiceGAAS |
"RiceGAAS is a rice genome automated annotation system. This system integrates programs for prediction and analysis of protein-coding gene structure." |
2183 |
| RMD |
"Rice Mutant Database (RMD) is an archive for collecting, managing and searching information of the T-DNA insertion mutants generated by an enhancer trap system." |
2417 |
| TropGENE DB |
"TropGeneDB is a database that manages genomic, genetic and phenotypic information about tropical crops. It is organised on a crop basis." |
2272 |
| GrainGenes |
"Graingenes is the international database for the wheat, barley, rye and oat genomes. " |
2402 |
| SoyGD |
"The Soybean GBrowse Database combines Perl MySQL database programming with Gbrowse to provide an integrated way of presenting soybean genomic features. " |
2231 |
| TAIR |
"The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana " |
7446 |
| AthaMap |
"AthaMap provides a genome-wide map of potential transcription factor and small RNA binding sites in Arabidopsis thaliana." |
2423 |
| CATMA |
"The aim of the Complete Arabidopsis Transcriptome MicroArray (CATMA) project was the design and production of high quality Gene-specific Sequence Tags (GSTs) covering most Arabidopsis genes" |
2305 |
| Lis (formerly MGI) |
"The mission of LIS is to enable productive applied and basic research in the legumes by relating data from multiple crop and model species, and by helping researchers traverse among various data types." |
2290 |
| base |
"RAD is a contig-oriented database for high-quality manual annotation of RGP, which can present non-redundant contig analyses by merging the accumulated PAC/BAC clones." |
2193 |
| Gramene |
"Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species." |
3657 |
| IRIS |
The International Rice Information System "is the rice implementation of the International Crop Information System (ICIS) which is a database system that provides integrated management of global information on genetic resources and crop cultivars" |
2430 |
| MaizeGDB |
"MaizeGDB is the community database for biological information about the crop plant Zea mays." |
3503 |
| PlantMarkers |
"PlantMarkers is a genetic marker database that contains a comprehensive pool of predicted molecular markers." |
2237 |
| MAtDB |
"The MAtDB aims to provide a comprehensive resource for Arabidopsis as a genome model that serves as a primary reference for research in plants and is suitable for transfer of knowledge to other plants, especially crops." |
2207 |
| Panzea |
"
"The Panzea Database contains the genotypic and phenotypic data and genetic marker information produced by the NSF-funded project 'Genetic Architecture of Maize and Teosinte'. " |
2133 |
| PlantGDB |
"PlantGDB is a database of molecular sequence data for all plant species with significant sequencing efforts" |
2737 |
| RAP-DB |
The Rice Annotation Project (RAP) database. |
3872 |
| Seed Genes |
"This project deals with genes that exhibit a seed phenotype when disrupted by a loss-of-function mutation" |
2412 |
| Oryzabase |
"The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan. The database is originally aimed to gather as much knowledge as possible ranging from classical rice genetics to recent genomics and from fundamental information to hot topics" |
5573 |
| TED |
"Tomato functional genomics database" |
2219 |
| WAtDB |
"wageningen arabidopsis thaliana database (watdb) is a new, web-accessible database with curated data on Arabidopsis thaliana mutants." |
2090 |
| AGNS |
"AGNS (Arabidopsis GeneNet supplementary) database is an Internet-available resource that provides access to description of the functions of the known Arabidopsis genes at various levels-the levels of mRNA, protein, cell, tissue, and ultimately at the levels of organs and the organism in both wild type and mutant backgrounds." |
2189 |
| PhytoProt |
"The general procedure behind PHYTOPROT consists in performing an "all-by-all" comparison of (putative) protein sequences with the BIOFACET software, building clusters of sequences (Mohseni-Zadeh et al., Recomb 2003) based on their similarity and finally displaying |
2282 |
| TIGR plant repeat database |
"The TIGR plant repeat database is a repository of repetitive sequences in plants." |
2294 |
|
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| Prokaryotic Databases |
|
| Site Name |
Description |
Clicks |
| DEG Database |
It is a Database of essential genes from bacteria and yeast |
2348 |
| EcoGene |
"EcoGene.org is a genome database and website dedicated to Escherichia coli K-12 substrain MG1655 that is revised daily using information derived from the biomedical literature and in-house analysis." |
2270 |
| LeptoList |
"A complete dataset of DNA and protein sequences derived from the paradigm strain L. interrogans serovar Lai, linked to the relevant annotations and functional assignments" |
2183 |
| DOOR |
It’s a "Complete and reliable operon database covering 2072 bacteria genomes and with overall accuracy of ~90% " |
2392 |
| PSORTdb |
"PSORTdb (part of the PSORT family) is a database of protein subcellular localizations for bacteria and archaea that contains both information determined through laboratory experimentation (ePSORTdb dataset) and computational predictions (cPSORTdb dataset)." |
2557 |
| Genolist |
"GenoList: an integrated environment for comparative analysis of microbial genomes" |
2244 |
| CyanoBase |
"CyanoBase is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, complete genome sequences, genome-scale experiment data, gene information, gene annotations and mutant information." |
2309 |
| GenProtEC |
"GenProtEC website was dedicated to the functions encoded by the Escherichia coli K-12 (strain MG1655) " |
2255 |
| IMG |
"The mission of the Integrated Microbial Genomes (IMG) system is to support the annotation, analysis and distribution of microbial genome and metagenome datasets sequenced at DOE's Joint Genome Institute (JGI). IMG is also open to scientists worldwide for the annotation, analysis, and distribution of their own genome and metagenome datasets, as long as they agree with the IMG data release policy and follow the metadata requirements for integrating data into IMG " |
5540 |
| MBGD |
"MBGD is a database for comparative analysis of completely sequenced microbial genomes, the number of which is now growing rapidly. The aim of MBGD is to facilitate comparative genomics from various points of view such as ortholog identification, paralog clustering, motif analysis and gene order comparison" |
4242 |
| OPERON |
It’s a site that allows us to "to detect and analyze conserved gene pairs - pairs of genes that are located close on the same DNA strand in two or more bacterial genomes. For each conserved gene pair", the algorithm "calculate an estimate of probability that the genes belong to the same operon" |
2320 |
| VirFact |
"Bacterial virulence factors and pathogenicity islands" |
2203 |
| 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" |
2140 |
| BSD |
"The Biodegradative Strain Database (BSD) is a freely-accessible, web-based database providing detailed information on degradative bacteria and the hazardous substances that they degrade, including corresponding literature citations, relevant patents and links to additional web-based biological and chemical data" |
2244 |
| ClostriDB |
"A database for Clostridium genome analysis." |
2057 |
| GenoBase |
"Public repository for Sequence Information, Proteome, Transcriptome, Bioinformatics, and Knowledge based on literature concerning E. coli." |
2187 |
| EHCO |
"EchoBASE is a relational database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. " |
2237 |
| EchoBASE |
"EchoBASE is a relational database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12." |
2055 |
| Extra-TRAIN |
"ExtraTrain is a database for exploring Extragenic space and Transcriptional information in bacteria and archaea." |
2136 |
| GeneDB |
"The GeneDB project is a core part of the Sanger Institute's Pathogen Genomics activities. Its primary goals are: to provide reliable access to the latest sequence data and annotation/curation for the whole range of organisms sequenced by the Pathogen group and to develop the website and other tools to aid the community in accessing and obtaining the maximum value from these data. |
2190 |
| Colibri |
"This server is constructed around a database dedicated to the analysis of the genome of Escherichia coli: Colibri.Its purpose is to collate and integrate various aspects of the genomic information from E. coli, the paradigm of Gram-negative bacteria." |
2270 |
| Essential Genes in E.coli |
"It provides links to data on essential genes in E. coli, and shows a short list of E. coli essential genes identified from the Neidhardt E. coli books " |
2917 |
| E. coli ASAP |
"ASAP is a relational database and web interface developed to store, update, and distribute genome sequences in conjunction with associated annotations and functional characterization data" |
2748 |
| UM-BBD |
"UM-BBD allows to Search for curated information on microbial catabolism and related biotransformations, primarily for environmental pollutants." |
2584 |
| EMGlib |
"The Enhanced Microbial Genomes Library (EMGLib) is a database system containing all the complete genomes sequenced from prokaryotic organisms (bacteria and archaea)" |
2131 |
| MetaGrowth |
"Metagrowth is a database aiming to guide experimental studies and in silico simulation studies on the culture conditions of obligate parasitic bacteria. " |
2121 |
| CIDB |
"The Chlamydia Interactive Database (CIDB) described here is the first database of its type that holds genomic, RT-PCR, microarray and proteomics data sets that can be cross-queried by researchers for patterns in the data." |
2154 |
| TIGR Microbial Database |
"The Comprehensive Microbial Resource (CMR) is a free tool that allows researchers to access all of the publicly available bacterial genome sequences completed to date" |
2099 |
| PromEC |
"PromEC is an updated compilation of E. coli mRNA promoter sequences. It includes documentation on the location of experimentally identified mRNA transcriptional start sites on the E. coli chromosome, as well as the actual sequences in the promoter region. " |
2001 |
| MeGX |
"Megx.net allows access to integrated environmental and (meta)genomic data intended for use in marine microbial ecology" |
2114 |
| PGTdb |
"PGTdb integrates microorganisms' growth temperature data from literature survey with their nucleotide/protein sequence, protein family and structure data from related databases." |
2217 |
| VBI Microbial Database |
"The VBI Microbial Database hosts data from different sources for a range of plant pathogenic oomycetes, fungi and bacteria, primarily those organisms under study at VBI" |
2168 |
| CyberCell database |
"The CyberCell database (CCDB) is a comprehensive collection of detailed enzymatic, biological, chemical, genetic, and molecular biological data about E. coli " |
2003 |
| ~CTOR db |
"Tractor_DB (v.2.0) contains a collection of computationally predicted Transcription Factors' binding sites in gamma-proteobacterial genomes" |
2310 |
| CampyDB |
"CampyDB is a database for Campylobacter genome analysis. It allows users to conduct search, blast, sequence pattern search and genome browsing." |
2189 |
| coliBase |
"xBASE2: a comprehensive resource for comparative bacterial genomics. It is a is a genome database aimed at helping laboratory-based bacteriologists make best use of bacterial genome sequence data, with a particular emphasis on comparative genomics." |
2259 |
| ISfinder |
"IS finder database provides a list of insertion sequences isolated from eubacteria and archae. It is organised into individual files containing their general features (name, size, origin, family.....) as well as their DNA and potential protein sequences." |
4656 |
| RegulonDB |
"RegulonDB is a database of the regulatory network of Escherichia coli K-12" |
2110 |
| Virulence Factors |
"a reference database for bacterial virulence factors." |
2138 |
|
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| Promoter and Transcription Factor DB |
|
| Site Name |
Description |
Clicks |
| ABS DB |
It is "a database of Annotated regulatory Binding Sites from orthologous promoters" |
2093 |
| TRED |
"TRED is a resource for studies on gene function and regulation. It provides cis-elements, such as promoters and binding motifs, and trans-elements, such as transcriptional factors (TFs)." |
2248 |
| DPInteract |
"DPInteract: A database on DNA-protein interactions." |
2286 |
| JASPAR |
"The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes." |
2252 |
| MPromDB |
"MPromDb (Mammalian Promoter Database) is a curated database that strives to annotate gene promoters identified from ChIP-Seq experiment results. " |
2218 |
| DBTBS |
"DBTBS is a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. " |
2207 |
| DoOP |
"DoOP is a database of eukaryotic promoter sequences (upstream regions), aiming to facilitate the recognition of regulatory sites conserved between species." |
2223 |
| EPD |
"The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally." |
2207 |
| TRANSCompel |
"TRANSCompel contains data on eukaryotic transcription facotrs experimentally proven to act together in a synergistic or antagonistic manner." |
2747 |
| TRANSF AC |
"TRANSFAC |
2367 |
| HTPSELEX |
"The HTPSELEX database contains sets of invitro selected transcription factor binding site sequences obtained with SELEX and high-throughput SELEX method." |
2151 |
| DBD |
"DBD is a database of predicted transcription factors in completely sequenced genomes." |
2804 |
| TRRD |
"TRRD is a unique information resource, accumulating information on structural and functional organization of transcription regulatory regions of eukaryotic genes." |
2117 |
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| QTL Database |
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| Site Name |
Description |
Clicks |
| QTL Matchmaker |
It "is a tool which addresses this problem. It allows for high throughput mapping of genes to known QTL and comparative genomics analysis between Homo sapiens, Mus musculus, Rattus norvegicus" |
2250 |
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| Ribosome Databases |
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| Site Name |
Description |
Clicks |
| IRESdb |
"IRES database is a comprehensive WWW resource for internal ribosome entry sites and presents currently available general information as well as detailed data for each IRES" |
2117 |
| IRESite |
"The IRESite database presents information about the experimentally studied IRES (Internal Ribosome Entry Site) segments. " |
2630 |
| RISSC |
"RISSC (Ribosomal Intergenic Spacer Sequence Collection) compiles more than 1600 entries of edited DNA sequence data from the 16S-23S ribosomal spacers present in most prokaryotes and organelles (e.g. mitochondria and chloroplasts) and where systematic searches for specific words can be conducted, as well as BLAST-type sequence searches." |
2099 |
| DRC |
"The Database of Ribosomal Cross-links (DRC) provides a complete collection of all the published data produced by cross-linking studies on the Escherichia coli ribosome, as well as on its components and functional ligands. " |
2050 |
| RID OM |
"The Ribosomal Differentiation of Medical Microorganisms (RIDOM) web-server is an evolving electronic resource designed to provide microorganism (bacteria, fungi, mycobacteria) differentiation services for medical identification needs." |
2323 |
| RDP-I1 |
"Ribosomal database project" |
7791 |
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| SNP |
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| Site Name |
Description |
Clicks |
| Database of Genomic Variants |
"The Database of Genomic Variants provides a useful catalog of control data for studies aiming to correlate genomic variation with phenotypic data." |
2714 |
| dbQSNP |
dbQSNP Public", is a repository of STS/SNP information obtained by "dbQSNP conductor". SSCP and sequence trace data are just a few clicks away, and thus, integrity of the data can be confirmed." |
2280 |
| JSNP |
"Japanese single nucleotide polymorphism identifies SNPs (single nucleotide polymorphisms in gene regions) distributed throughout the human genome, to make the information related to these SNPs available to the public and to develop analytical tools for polymorphisms. |
2264 |
| ALFRED |
"The ALlele FREquency Database is a resource of gene frequency data on anthropologically defined human population samples readily available to the scientific community and to link these polymorphism data to the molecular genetics-human genome databases." |
2517 |
| dbRIP |
"dbRIP is a highly integrated database of Retrotransposon Insertion Polymorphism (RIPs) in human." |
2223 |
| TopoSNP |
"TopoSNP produces an interactive visualization of disease and non-disease associated non-synonymous single nucleotide polymorphisms (nsSNPs) and displays geometric and relative entropy calculations." |
2237 |
| HGVbase |
"GWAS Central provides a centralized compilation of summary level findings from genetic association studies, both large and small." |
2521 |
| HGVS Databases |
"The Human genome Variation society maintains comprehensive lists of databases to foster discovery and characterization of genomic variations including population distribution and phenotypic associations." |
8874 |
| SNPeffect |
"SNPeffect is a database for phenotyping human single nucleotide polymorphisms (SNPs)" |
2256 |
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| Vector Databases |
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| Site Name |
Description |
Clicks |
| UniVec |
"UniVec is a database that can be used to remove the vector contamination from the DNA sequences" |
3079 |
| VectorDB |
"VectorDB contains annotations and sequence information for many vectors commonly used in molecular biology." |
2139 |
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| Virus Databases |
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| Site Name |
Description |
Clicks |
| HCVDB |
" The euHCVdb is mainly oriented towards protein sequence, structure and function analyses and structural biology of HCV " |
2317 |
| Influenza Virus resource |
"Influenza Virus Resource presents data obtained from the NIAID Influenza Genome Sequencing Project as well as from GenBank, combined with tools for flu sequence analysis, annotation and submission to GenBank." |
2144 |
| Poxvirus.org |
"Goals for the PBR include facilitation of basic research as well as the development of novel antiviral therapies, vaccines against human orthopoxvirus infections, new approaches for the environmental detection of virions, and methods to accomplish more rapid diagnosis of disease." |
2212 |
| Viral Bioinformatics Resource Centre |
"Viral Bioinformatics resource centre provides Databases of viral genomic information (genes, gene families, and genomes) and Software to perform comparative genomics analyses" |
2443 |
| VirOligo |
"VirOligo is a database of virus-specific oligonucleotides." |
2225 |
| VIDA |
"Virus Database at University College London (VIDA) contains a complete collection of homologous protein families derived from open reading frames from complete and partial virus genomes. For each family you can get an alignment of the conserved regions, functional and taxonomy information, and links to DNA sequences and structures." |
2352 |
| VIPERdb |
"VIPERdb is a database for icosahedral virus capsid structures . The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. " |
3152 |
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| Other Structural DB |
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| Site Name |
Description |
Clicks |
| ASD |
"Allosteric Database (ASD) provides a central resource for the display, search and analysis of the structure, function and related annotation for allosteric molecules." |
2591 |
| YDPM |
"The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell." |
2291 |
| THGS |
"Transmembrane Helices in Genome Sequences (THGS v2) is an interactive web based database which has been developed to search the transmembrane helices in the user-defined genome available in the Genome Database (GDB)." |
2217 |
| Structure superposition Database |
"The SSD has been developed to address the need for resources and tools for understanding large sets of superpositions in order to understand evolutionary relationships and to make predictions of function." |
2218 |
| MolMovDB |
"Database of Macromolecular Movements with Associated Tools for Flexibility and Geometric Analysis describes the motions that occur in proteins and other macromolecules" |
2242 |
| E-MSD |
"PDBe is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures." |
4130 |
| 1MB Jena Image library |
"The Jena Library of Biological Macromolecules (JenaLib) is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis." |
2193 |
| MMDB |
"The Molecular Modeling Database (MMDB) is a database of experimentally determined 3D-dimensional biomolecular structures and hosted by the National Center for Biotechnology Information" |
2213 |
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