Bioinformatics Tools and Software
| Primer Designing |
|
| Site Name |
Description |
Clicks |
| FastPCR |
"FastPCR is an integrated tool for PCR primers or probe design, in silico PCR, oligonucleotide assembly and analyses, alignment and repeat searching". This program can be downloaded and run in PCs. |
6384 |
| AutoPrime |
Autoprime is a very useful software for designing Reverse Transcription Real Time PCR (Q-RT-PCR) primers that are specific to the exon-intron boundaries. |
3774 |
| Primer3 (version 0.4.0) |
It is a freely available online software for designing primers and probe from a DNA sequence. It’s a very popular software due to avilability of several parametrs to design primers with high specificity and accuracy. |
7444 |
| PCR PRIMER DESIGN AND REACTION OPTIMISATION |
It’s a very useful site to learn about the pros and cons of factors affecting PCR. |
3649 |
| The PCR Suite |
It’s an online primer designing software, hosted by UCSC, that allows users to design primers specific to various types of templates, viz. overlapping amplicons on a template, primers around SNP (in a GenBank), primers flanking exons and cDNA. |
3611 |
| Uniprime2 |
It is a website for universal primer designing. |
3806 |
| Primo Pro 3.2 |
Its another online primer designing software. Its notable feature is that it can reduce background noise by exercising check on mispriming on non-target DNA sequence. It also "introduces a batch mode option for high throughput PCR primer design". |
3689 |
| MethPrimer |
Its very useful site for designing primers for methylation PCR (Denatured, single stranded DNA (ssDNA) is modified with sodium bisulfite "followed by PCR amplification using two pairs of primers, with one pair specific for methylated DNA; the other unmethylated DNA"). |
3240 |
| IDT Antisense Design |
To synthesize antisense oligos for a specific target sequence of interest. |
2963 |
| PrimerBLAST |
Extensively used for designing primer and checking the specificity of a given primer. |
6575 |
| Gene Fisher |
"GeneFisher is an interactive web-based program for designing degenerate primers". The underlying assumption is "assumption that genes with related function from different organisms show high sequence similarity, degenerate primers can be designed from sequences of homologues genes". This assumption "leads to isolation of genes in a target organism using multiple alignments of related genes from different organisms" |
3245 |
| PrimerQuest |
Online primer designing tool provided by IDT |
4905 |
| GenomePRIDE 1.0 |
"GenomePRIDE is primer design program that designs PCR primers or long oligos on an annotated sequence" |
2664 |
| RE specific primer desining |
"PCR Designer for Restriction Analysis of Sequence Mutations" |
2604 |
| CODEHOP |
"The COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP) program is hosted by the Fred Hutchinson Cancer Research Center in Seattle, Washington and designs PCR (Polymerase Chain Reaction) primers from protein multiple-sequence alignments" |
3151 |
| Oligos 6.2 |
"The program helps to design primer combinations given one fixed primer" |
2730 |
| Primo Pro 3.4 |
A java enabled online primer designing tool. |
2680 |
| Primo Degenerate3.4 |
"Primo Degenerate 3.4 designs PCR primers based on a single peptide sequence or multiple alignments of proteins or nucleotides. For degenerate primers, the probability of binding to the target is proportional to the effective concentration of the specific primer" |
2835 |
| Oligo.Net |
"OLIGO Primer Analysis Software is the essential tool for designing and analyzing sequencing and PCR primers, synthetic genes, and various kinds of probes including siRNA and molecular beacons. Based on the most up-to date nearest neighbor thermodynamic data, Oligo's search algorithms find optimal primers for PCR, including TaqMan, highly multiplexed, consensus or degenerate primers. Multiple file batch processing is possible. It is also an invaluable tool for site directed mutagenesis" |
3998 |
| AlleleID |
"AlleleID® is a comprehensive desktop tool designed to address the challenges of bacterial identification, pathogen detection or species identification" |
3629 |
| Array Designer 2 |
Its an Oligo and cDNA Microarray Design Software. "It designs probes for SNP detection, microarray gene expression and gene expression profiling. In addition, comprehensive support for tiling arrays and resequencing arrays is available" |
9286 |
| LAMP Designer |
"LAMP Designer designs efficient primers for Loop-Mediated Isothermal Amplification assays, that amplify DNA and RNA sequences at isothermal conditions, eliminating the necessity of a PCR setup". |
3321 |
| Beacon Designer |
"Beacon Designer™ automates the design of real time primers and probes". |
3058 |
| NetPrimer |
It’s an efficient primer analysis software that can be used for determining the featurs of the secondary structures of the generated primer-sequences. |
3683 |
| SimVector |
Its "an exceptional tool for drawing publication and vector catalog quality plasmid maps, carrying out restriction analysis and designing cloning experiments" |
3020 |
| Primer Premier |
Primer Premier is one of the "most comprehensive software to design and analyze PCR primers". Primers can be designed for standard PCR, SNP genotyping assays, Multiplexing assyas, along with checking the secondary structures of the designed primers. |
4232 |
| Meth Primer |
"MethPrimer is a program for designing bisulfite-conversion-based Methylation PCR Primers" |
3193 |
| Web Primer |
A simple tool for primer desining for PCR or sequencing. |
3016 |
|
Top of Page
| Primer Properties Checking |
|
| Site Name |
Description |
Clicks |
| Oligo Analyzer Version 3.1 (IDT) |
The secondary structures produced by the primer(s) can be checked, along with the Gibbs free energy required to produce these structures can be calculated using online Oligo Analyzer Version 3.1 (of IDT). |
6342 |
| OligoAnalyzer 3.1 |
This online tool is provided by IDT for analyzing the properties of the oligos as well as for predicting the likelihood of self and heterodimer formation by oligos. |
5157 |
| Oligonucleotide Properties Calculator |
Calculates base-count, thermodynamic properties (ΔS & ΔH), Tm, GC% values of a given oligo. |
2884 |
| Oligonucleotide Properties Calculator |
It’s a very useful, oligonucleotide proterties calculator. It displays the reverse complementary sequence, physical properties (length, molecular weight, GC%), Tm, Thermodynamic constants and hairpin & self-dimer production by a given primer/ sequence. |
4044 |
| UnaFold |
The likelihood of secondary structure formation by the single-stranded target is checked by UnaFold software of IDT (freely available online). |
2757 |
| Oligo. Properties Calc. |
Online tool to calculate several features (physical constants, Thermodynamic constants, hairpin formation etc) of one or a pair of oligo nucleotide sequence(s). |
3298 |
| Oligo Tm Determination |
Calculates the melting temperatur of the oligos |
2642 |
|
Top of Page
| Restriction analysis |
|
| Site Name |
Description |
Clicks |
| RestrictionMapper |
Online, freely available tool for mapping restriction endonuclease sites on a DNA sequence. |
5767 |
| Webcutter 2.0 |
Another RE site detection software (online, free) for linear and circular DNA. |
3568 |
| Mapper |
Java platform based online software to map the RE sites on a target sequence. |
3448 |
| NEB Cutter |
This software is RE site mapper, hosted by New England Biolabs. |
3079 |
| Web Map |
Web Map software maps the RE sites for a given sequence (circular or linear). It can also produce the reverse complementary of the input sequence, which can be assigned for mapping of RE sites. |
4593 |
|
Top of Page
| RNAi |
|
| Site Name |
Description |
Clicks |
| GeneCopoeia |
"GeneCopoeia, Inc. is a US-based manufacturer and provider of genomics and proteomics products and services for academic and governmental research institutes, pharmaceutical and biotechnology industry". "GeneCopoeia offers comprehensive tools for microRNA (miRNA) functional analysis so researchers can detect, express, validate or knockdown microRNA of interest confidently. All known human, mouse and rat microRNA in miRBase covered". |
2979 |
| RNAi Atlas |
"RNAiAtlas provides a siRNA oligonucleotide data from different sources and companies like Dharmacon (ThermoFisher), Qiagen, Ambion, esiRNA for human, and visualize interactions between siRNA oligo and predicted off-target". |
2760 |
| Comparative RNA Website and Project |
"The Comparative RNA Web (CRW) Site disseminates information about RNA structure and evolution that has been determined using comparative sequence analysis". |
3229 |
| RNAfold |
"The RNAfold web server will predict secondary structures of single stranded RNA or DNA sequences. Current limits are 7,500 nt for partition function calculations and 10,000 nt for minimum free energy only predicitions". |
2722 |
| RNAhybrid |
"RNAhybrid is a tool for finding the minimum free energy hybridisation of a long and a short RNA" |
2767 |
| miRNAMap |
miRNAMap 2.0 is a collection of "experimental verified microRNAs and experimental verified miRNA target genes in human, mouse, rat, and other metazoan genomes" |
2571 |
| siRNA Designing-BOCK-iT RNAi Designer |
Online siRNA designing tool from Invitrogen |
3034 |
| Prediction of miRNA Targets (Mammals) |
The tool "searches for predicted microRNA targets in mammals" |
3792 |
| E-RNAi |
RNAi construct designer |
2358 |
| miRNA Targets and Expression db |
"Predicted microRNA targets & target downregulation scores. Experimentally observed expression patterns" |
2530 |
| miRNa Body map (Human) |
"The microRNA body map is a repository of RT-qPCR miRNA expression data and functional miRNA annotation in normal and diseased human tissues" |
2410 |
| siRNA Design: How to |
A short introduction to siRNA Designing Steps |
2522 |
| miRNA Target Gene Prediction |
"This website provides access to 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs" |
2425 |
| siRNA Wizard v. 3.1 |
"InvivoGen's siRNA Wizard™ is a software designed to help you select siRNA/shRNA sequences targeting your gene(s) of interest. This program selects siRNA/shRNA sequences that match criteria suggested by studies of RNA interference and which will have the best expression rate in psiRNA vectors.". |
2725 |
| siDesign- Thermo Scientific |
"The siDESIGN Center is an advanced, user-friendly siRNA design tool, which significantly improves the likelihood of identifying functional siRNA.One-of-a-kind options are available to enhance target specificity and adapt siRNA designs for more sophisticated experimental design" |
2504 |
| RNAi Explorer- GeneLink-siRNA |
Adesigning tool for siRNA |
2836 |
| RNAi Explorer- GeneLink-shRNA |
shRNA designing online tool. |
2623 |
|
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| Bioinformatics Work |
|
| Site Name |
Description |
Clicks |
| BLAST |
Basic local alignment search tool, provided by NCBI. |
3654 |
| Translate a DNA Sequence |
It’s a Java based free online software, to translate a given input DNA sequences and display one (at a time ) of the six possible reading frame according to the selection made by the user. It also displays the graphical output for all the six reading frames together. |
3236 |
| ORF Finder |
"The ORF Finder (Open Reading Frame Finder) is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database". |
3800 |
| Ensembl Variant Effect Predictor |
"This tool takes a list of variant positions and alleles, and predicts the effects of each of these on overlapping transcripts and regulatory regions annotated in Ensembl. The tool accepts substitutions, insertions and deletions as input". |
2846 |
| DAVID v. 6.7 |
The Database for Annotation, Visualization and Integrated Discovery (DAVID ) v6.7 “provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genesâ€. |
3521 |
| ReadSeq-Sequence Format Conversion Tool |
Online tool for conversion of sequence format. |
2967 |
| READSEQ |
Converts input DNA/AA sequence to specified output format (Input format is determined automatically). |
10136 |
| BioEdit |
"BioEdit is a biological sequence alignment editor written for Windows 95/98/NT/2000/XP/7". One can download and then work with the molecular sequences for alignment, restriction mapping, RNA analysis, translation, graphical viewing of electropherogram etc. |
3339 |
| DNA/RNA GC Content Calculator |
One can calculate the GC content of a nucleotide sequence. |
3652 |
| PEDANT |
"The pedant genome database provides exhaustive automatic analysis of genomic sequences by a large variety of bioinformatics tools" |
2611 |
| SIDDbase 1.0a.ws1 |
"SIDDbase-WS is a SOAP based Web Service" that "provides interoperable access to the SIDD software, and access to the repository of stored results from calculations previously performed on complete bacterial genomes" |
2327 |
| SANBI Tools |
An array of online tools (dPORE-miRNA, TcoF, PROMEX etc) are avilable which are maintained by South African National Bioinformatics Institute. |
2335 |
| VBI resources |
This site of Virginia Bioinformatics Institute maintains several tools for bioinformatics analysis viz. "Analysis of Dynamic Algebraic Models", "Complex Pathway Simulator", "Genome Reverse Compiler" etc. |
2600 |
|
Top of Page
| Dotplot |
|
| Site Name |
Description |
Clicks |
| Dotlet |
Dotlet is a free online software used as a tool for diagonal plotting of sequences. |
2985 |
| Dotplot(+) |
Dot-plot(+) software is used to identify the overlapping portions of two sequences and to identify the repeates and inverted repeats of a pericular sequence. |
3047 |
| Dotter |
Dotter is a graphical dotplot program for detailed comparison of two sequences. It runs on MAC, Linux, Sun solaris and Windows OS. |
3326 |
|
Top of Page
| Sequence Alignment |
|
| Site Name |
Description |
Clicks |
| CINEMA 2.1 |
CINEMA stands for Colour INteractive Editor for Multiple Alignments. It’s a free software for sequence alignment with color editor. |
3621 |
| MACAW |
This links enables you to download Multiple Alignment Construction & Analysis Workbench (MACAW) software. This program is used for "locating, analyzing, and editing blocks of localized sequence similarity among multiple sequences and linking them into a multiple alignment". |
3317 |
| SIM4 |
A stand alone program designed to run on Unix based system. It is used for aligning an expressed DNA sequence with a genomic sequence, allowing for introns. |
2840 |
| PILUP |
It "creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments. It can also plot a tree showing the clustering relationships used to create the alignment". |
2780 |
| JALVIEW |
It is a "multiple alignment editor written in Java". It is used in EBI Clustalw, Pfam protein domain database, however, it is "available as a general purpose alignment editor and analysis workbench". |
5117 |
| SIM |
It is an online "program which finds a user-defined number of best non-intersecting alignments between two protein sequences or within a sequence". |
3075 |
| Clustal Omega |
the latest form of Clustal alignment program. It is online and command-line based. The distinguishing feature of Clustal-omega is its scalability, as several thousands of medium to large sized sequences can be aligned simultaneously. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to the previous versions. The algorithm uses seeded guide trees and HMM profile-profile progressive alignments. |
6256 |
| Clustal W |
A very popular site for pairwise and multiple sequence alignment. . It runs in Windows, Linux/Unix and Mac operating systems. |
3640 |
| CLUSTAL X |
Latest version of ClustalX 2.0 is provided by "Plate-Forme Bio-Informatique de Strasbourge", along with detail instructions (help) for operating ClustalX. Besides, this site also provides online tools (ciz. Actin Related Proteins Annotation server, EMBOSS, Gene Ontology Annotation, SAGE experimet parameters, GPAT etc) and database (SRS, BAliBase, InPACT), Documentation (tutorials to elucidate the parameters of Clustal, GCG, EMBOSS, Bioinformatics protocols etc). |
2891 |
| LALIGN |
Lalign is considered as one of the most reliable tool for local alignment of nucleotide and amino acid sequences. |
2890 |
| LALIGN |
Online free tool for finding local alignment between two sequences (provided in stipulated input format, viz. plain text without header line, Swiss-Prot ID, TrEMBL ID, EMBL ID, EST ID etc). |
3111 |
| FASTA |
This server is hosetd by the University of Virginia, USA. It harbours a multiple online software for sequence (nucleic acid and mino acid) comparison, local and global alignment, Hydropathy plotting and protein secondary structure prediction. |
3849 |
| MAFFT version 6 |
"MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences)". |
4649 |
| T-cofee |
Tree-based Consistency Objective Function For alignment Evaluation (T-Coffee) is another popular multiple sequence alignment program, developed by Cedric Notredame, CRG Centro de Regulacio Genomica (Barcelona). It allows combining results obtained from several alignment methods. The URL is http://www.ebi.ac.uk/Tools/msa/tcoffee/. The default output format is Clustal, while it accepts sequences in PIR and FASTA format. |
3499 |
|
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| Phylogenetics |
|
| Site Name |
Description |
Clicks |
| Phylogeny Inference Package |
"PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables". |
3379 |
| Phylogeny Inference Package (v. 3.5) |
"This is a FREE package of programs for inferring phylogenies and carrying out certain related tasks. At present it contains 31 programs, which carry out different algorithms on different kinds of data". |
2842 |
| Molecular Evolution Geneti Analysis (v. 5.1 beta) |
A handy package for analysing sequence data for pair-wise and multiple sequence alignment, phylogenetic tree (include neighbor-joining, maximum parsimony, UPGMA, Maximum likelihood and mimimum evolution based) construction and estimation of evolutionary parameters. |
7708 |
| List of phylogenetics software |
List of online/downladable software for phylogenetic tree construction, displayed with links in Wikipedia page. |
4388 |
|
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| Proteomics |
|
| Site Name |
Description |
Clicks |
| Expert Protein Analysis System |
“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 etcâ€. |
2811 |
| RASMOL Home page |
"This site is provided for the convenience of users of RasMol and developers of open source versions of RasMol". |
2952 |
| Expasy-Translate tool |
It’s an online tool that "allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence". |
2716 |
| Protein Data Bank |
PDB is an "information portal to biological macromolecular structure". "The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies". |
3263 |
| RASMOL |
RasMol is a molecular visualization tool for protein in 3-dimension. |
4789 |
| Structural Biology Software Database |
Harbors links to several software for docking |
3233 |
| MS Utils |
Maintains links to several platforms, pipelines, libraries, software for visualization as well as software for proteomic data analysis,. |
3501 |
| Protein Tertiary Structure |
This site contains links to several software for "calculating and displaying the 3-D structure of oligosaccharides and proteins. With the two protein analysis sites the query protein is compared with existing protein structures as revealed through homology analysis". |
4612 |
| Structural Bioinformatics Group |
This is the structural bioinformatics related page maintained by Imperial College London. This site can be used for several purpose, viz. "analysis of protein structure and function with the aim of deriving evolutionary insights, modelling and comparison of biology networks to provide insights into Systems Biology, modelling of the activity and toxicity of small molecules as an aid to the design of novel drugs". |
3039 |
|
Top of Page
| Gene Prediction |
|
| Site Name |
Description |
Clicks |
| Promoter 2.0 Prediction Server |
Promoter2.0 predicts transcription start sites of vertebrate PolII promoters in DNA sequences. It has been developed as an evolution of simulated transcription factors that interact with sequences in promoter regions. It builds on principles that are common to neural networks and genetic algorithms. |
3589 |
| Splice Predictors |
A method to identify potential splice sites in (plant) pre-mRNA by sequence inspection using Bayesian statistical models. |
2971 |
| GeneMark |
GeneMark is a “family of gene prediction programs developed at Georgia Institute of Technology, Atlanta, Georgia, USAâ€. |
3807 |
| HMMgene 1.1 web server |
"HMMgene is a program for prediction of genes in anonymous DNA". "The program predicts whole genes, so the predicted exons always splice correctly. It can predict several whole or partial genes in one sequence, so it can be used on whole cosmids or even longer sequences". |
2949 |
| GAS |
GAS is UNIX or DOS based downloadable, command-line oriented "integrated computer program designed to automate and accelerate the acquisition and analysis of genomic data". |
2639 |
| GENSCAN |
GENSCAN is a freely available software used for "identification of complete gene structures in genomic DNA". Genscan can be used "for predicting the locations and exon-intron structures of genes in genomic sequences from a variety of organisms". |
3203 |
| Glimmer |
Glimmer (Gene Locator and Interpolated Markov ModelER) is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. |
3348 |
| Genome Bioinformatics Research Lab |
The site harbors"geneid" program which is used to "predict genes, exons, splice sites and other signals along a DNA sequence". This site is also hyperlinked with "Gene prediction on whole genome" which is a "precomputed whole genome prediction data sets". |
3155 |
| Webgene |
This site maintails several online "tools for prediction and analysis of protein-coding gene structure". |
2794 |
| geneid |
"geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure". |
3201 |
| mgene |
"mGene is a computational tool for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences". |
2808 |
| geneprediction.org |
|
2729 |
|
Top of Page
| Genome Browser |
|
| Site Name |
Description |
Clicks |
| Ensembl Genome Browser |
"The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online". |
3059 |
| Ensemble |
Ensemble, a genome browser like NCBI and UCSC, is a centralised repository of the Whole Genome Sequence of human and other species (vertebrate and model organisms). |
3568 |
| UCSC Human Genome Browser |
Its an interactive genome browser dedicated to human genome sequence. |
3326 |
| UCSC Genome Browser |
This is an “on-line genome browser hosted by the University of California, Santa Cruz (UCSC). It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotationsâ€. |
2616 |
|
Top of Page
| Multiple Software Resources |
|
| Site Name |
Description |
Clicks |
| Software wURLd |
Bio-wURLd is a searchable, user-maintained collection of URL's related to bioinformatics, biochemistry, and molecular biology. It comprises biocatalogues, other software or a link enlsiting the bioinformatics software. |
2492 |
| Swiss Institute of Bioinformatics |
"The SIB Swiss Institute of Bioinformatics is an academic, non-profit foundation recognised of public utility". SIB "provides high quality bioinformatics services to the national and international research community". |
6058 |
| ExPASY Resource Portal |
A resource portal supported by Expert Protein Analysis System and Swiss Institute of Bioinformatics for analysing bioinformatics data. |
2891 |
| Multi-Proteomics Suite |
A site that provides several databases pertaining to conserved proteins, motifs as well as tools for protein structure visualization and motif discovery. |
2628 |
| Webserveres developed by Dr. GPS raghava at IMTECH, India |
A very useful site for obtaining several online tools viz. Genome annotation, Structure prediction, Functional annotation, vaccine design, Databases etc. |
3040 |
| Emboss Align |
The European Molecular Biology Open Software Suite (EMBOSS) "is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community". Some of the applications are prophet (Gapped alignment for profiles), infoseq (Displays some simple information about sequences), water (Smith-Waterman local alignment), pepstats (Protein statistics) etc. |
3087 |
| geneinfinity |
This site contains description and links to various sites pertaining to Protein Secondary Structure. It is a hub for getting a quick look at several servers and metaservers that harbor databases and/or tools for prediction of protein secondary structures. |
2994 |
| Genome Tools |
"The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools†which consists of several modules". |
3741 |
| Bioinformatics Software |
“Softberry, Inc. is a leading developer of software tools for genomic researchâ€. The various areas covered by this company are: Genome annotation, Functional site identification in DNA and Proteins, Sequence database managing, Genome comparison, Expression data analysis, Protein structure prediction and Protein compartment (destination) prediction. |
3166 |
| Bioinformatics programs and databases |
A collection (alphabatically arranged) of evaluated bioinformatics programs and databases. |
2780 |
| Sequence Manipulation Suite-2 |
A suite available for almost all possible manipulation work that can be done with a given DNA or amino acid sequence, viz. Format change, Sequence splitting, CpG island detection, ORF fnding, Pairwiase alignment, RE-Digestion, in silico mutation etc. |
2840 |
| NRSP-8 Bioinformatics Online Tools |
Explore and utilize several bioinformatics tools. |
2693 |
| Gel Compar II (Paid multimodule, stand alone software) |
It’s a commercial product. "GelCompar II consists of the Basic Software and 5 modules: Cluster analysis, Identification & Libraries, Comparative Quantification and Polymorphism Analysis, Dimensioning techniques & Statistics, and Database Sharing Tools". |
2982 |
| Bioinformatics Links Directory |
Its also a very useful site that harbors the links to all possible sites pertaining to computer (for bioinformatics), molecular sequences, expression, organisms, literature pertaining to bioinformatics etc. |
7888 |
| Biological software developped at the Institut Pasteur |
Several useful bioinformatics tools have been developed and have been made available to the scientific community. Some of the software are: sequence structure evaluation, NMR calculation, Fast databank entries retriever etc. |
2622 |
| BUBS- multi software tools |
The "Bielfeld University Bioinformatics Server" provides several online bioinformatics tools Genome Comparison, Alignments, Primer Design, RNA Studio, Evolutionary Relationships, protein docking, image processing for microarrays etc. |
2579 |
| Computational Biology at ORNL |
The Computational Biology and Bioinformatics Group of the Biosciences Division of Oak Ridge National Laboratory provides data and bioinformatics tools for prokaryotic and some eukaryotic genome and related analysis. The tools are "Gene Channel", "Generation Microbial Gene Prediction System", "Grail (Microbial Gene Prediction System Internet Linked", "Genome Analysis Pipeline" etc. |
2550 |
| Biocomputing Tutorials |
The site harbors a number of biocomputationa onlinel tools (Cleaner, Translator, NetPlasmit, Aligner, PatSearch etc for nucleotide and protein sequences) and half a dozens of software. |
3003 |
| PROMOTERS & TERMINATORS |
This site maintains links for different software and tools (viz. PromScan, SCOPE, Promoser, Arnold, WebGesTer) for scanning, predicting promoters and transcription terminators in Eukaryotes and Prokaryotes. |
3954 |
| Multiple tools for alignments |
This site provides several links for pairwise and multiple alignments. |
4613 |
| Galaxy Platform |
"Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses". |
4173 |
| GreenGenes (16srRNA sequence Alignment) |
The greengenes web application provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. The data and tools presented by greengenes can assist the researcher in choosing phylogenetically specific probes, interpreting microarray results, and aligning/annotating novel sequences. |
3247 |
| Science for Society |
An wonderful site that maintains links to several stand-alone, downloadable software as well as online software/tools for proteomics, molecular docking, modelling, chemistry tools, cheminformatics, as well as some databases. |
2566 |
| SDSC Biology Workbench |
"The Biology WorkBench is a web-based tool for biologists. The WorkBench allows biologists to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems" |
2445 |
| CSIR Informatics Portal |
This page is maintained by CSIR and harbors the software/tools developed for bioinformatics analysis. |
2651 |
| VLS3D |
This page maintains a "list of in silico drug design online services, standalone and related databases. It is manintained by Dr. B. Villoutreix, research director at the French National Medical Research Institute (Inserm)" |
2768 |
| User:Jarle Pahr/: Bioinformatics |
This page harbors several "links and notes regarding bioinformatics". This is a very useful link since a user can get link to almost all aspects of bioinformatics resources. |
16203 |
|
Top of Page
| Gel Analyzing Software |
|
| Site Name |
Description |
Clicks |
| Gel-Quant software |
The "Gel-Quant" software is used to analyse one dimensional gel images. The gel image is saved in "bitmap" format, following electrophoresis and scanning the gel. |
3224 |
| Gelcompar II V. 7.1 |
For analysing 1D Gel |
3496 |
|
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| Protein Structure Prediction |
|
| Site Name |
Description |
Clicks |
| I-TASSER Online |
I-TASSER is an online bioinformatics platform for predicting protein structure vis-à-vis funtion. It has been developed by Zhang Lab (University of Michigan) . It has topped the in CASP ranking of structure prediction during the years 2007 to 2010. |
4465 |
| PHYRE2 |
Protein Homology/AnalogY Recognition Engine (PHYRE) is a non-commercial, very popular online protein structure prediction (homology modelling) server. The user friendly GUI is very helpful for the novice in the field of protein structure prediction. |
3113 |
| MODELLER |
The homology modeling of Protein 3D structures can be done using downloadable software “MODELLER”. It can also be used for following protein structure based applications: databases search for amino acid sequences, Sequence and structural alignments clustering, de novo modeling of structural loops, model-optimization against user defined objective function and so on. |
4139 |
| SwissModel |
It is a fully automated protein structure homology-modeling server. One needs to register and then log in to create own work space. |
2861 |
| QUARK Online |
It is online software that applies QUARK algorithm for ab initio protein folding vis-à-vis structure prediction. It is another eminent online tool of Zhang lab that has secured esteemed ranking in CASP |
3048 |
| HHPred |
Homology detection & structure prediction by HMM-HMM: used for sequence database searching and structure prediction. It is fast enough and more sensitive in finding remote homologs. HHpred is performs pairwise comparison of profile hidden Markov models (HMMs). It can produce pairwise query-template sequence alignments, merged query-template multiple alignments & 3D structural models calculated by the MODELLER software from HHpred alignments |
2898 |
| RaptorX |
Another efficient protein structure prediction server that predicts the secondary & 3D protein structure. Besides, it also predicts solvent accessibility and disordered regions, assigns the following confidence scores to indicate the quality of a predicted 3D model. It has been developed by Xu Group of Toyota Technological Institute at Chicago. RaptorX-Binding, another tool available in the homepage of RaptorX is used for model-assisted protein binding site prediction. |
3486 |
| Robetta |
Robetta (Beta Version) of Baker Lab, Washington, USA, is a full-chain protein structure prediction tool. It can be used both for ab initio and comparative approaches for protein structure prediction. |
3799 |
| YASARA |
Yet Another Scientific Artificial Reality Application (YASARA) is used for predicting the rotamers (protein side-chain conformations) starting with single point mutations to complete homology models of proteins. |
2863 |
| Statistical Analysis of Protein Sequences (SAPS) |
It performs several statistcialanalyis of the physiochemical properties and other features of the protein sequenc, viz. compositional analysis, charge distributional analysis, distribution of other amino acid types, repetitive structures, multiplets, periodicity analysis |
2501 |
| Protscale |
"ProtScale allows you to compute and represent the profile produced by any amino acid scale on a selected protein". |
2395 |
| Bioinformatics Tools for Protein Structure Analysis |
Harbors links to several bioinformatics tools for protein structure prediction and visualization. |
2885 |
| Mobyle 1.5 |
This site maintains a number of online bioinformatics programs (assembly, database, display, hmm, phylogeny, protein, sequence, structure etc), workflows (alignment, db, phylogeny) and tutorial |
2699 |
| Modbase |
It’s a database for "comparative protein structure models". The pipeline used is ModPipe. |
2848 |
| SIMPA96 Secondary Structure Prediction |
An online to predict secondary structure of protein |
2394 |
| SOPMA |
Its an online protein Secondary structure prediction tool |
3602 |
| DeepView: SWISS PDBViewer v. 4.1 |
"Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface" |
2440 |
| WHA T IF |
What If "is a versatile molecular modelling package that is specialized on working with proteins and the molecules in their environment like water, ligands, nucleic acids, etc". The web interface provides a number of tools viz. Structure validation, Analyse a residue, Protein analysis, 2-D graphics, 3-D graphics, Hydrogen (bonds), Rotamer related, Docking, Crystal symmetry, mutation prediction etc. |
2531 |
| SWISS Model |
"SWISS-MODEL is a fully automated protein structure homology-modelling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists worldwide" |
2427 |
| Compute pl/Mw |
The tool "compute pI/Mw is a tool which allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of UniProt Knowledgebase (Swiss-Prot or TrEMBL) entries or for user entered sequences" |
4084 |
| Peptide Mass |
This online tool of ExPASy "PeptideMass cleaves a protein sequence from the UniProt Knowledgebase (Swiss-Prot and TrEMBL) or a user-entered protein sequence with a chosen enzyme, and computes the masses of the generated peptides. The tool also returns theoretical isoelectric point and mass values for the protein of interest" |
4487 |
| ProtParam |
"ProtParam is a tool which allows the computation of various physical and chemical parameters for a given protein stored in Swiss-Prot or TrEMBL or for a user entered sequence. The computed parameters include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY) " |
5285 |
| Secondary Structure Prediction Tools |
"These are a collection of protein secondary structure analysis and information sites" |
2334 |
| CPHModels 3.2 Server |
"CPHmodels 3.2 is a protein homology modeling server. The template recognition is based on profile-profile alignment guided by secondary structure and exposure predictions" |
2675 |
| EsyPred3D |
"ESyPred3D is an automated homology modeling program. The method gets the benefit of the increased alignment performances of an alignment strategy that uses neural networks". |
2938 |
| Mol. Modelling Database (MMDB) |
It harbors "experimentally resolved structures of proteins, RNA, and DNA, derived from the Protein Data Bank (PDB), with value-added features such as explicit chemical graphs, computationally identified 3D domains (compact substructures) that are used to identify similar 3D structures, as well as links to literature, similar sequences, information about chemicals bound to the structures" |
25269 |
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Top of Page
| Drug Designing |
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| Site Name |
Description |
Clicks |
| Drug Designing |
This webpage maintains several entries to drug-designing. One can learn, and make use of these software/ links. |
3536 |
| Click2Drug |
"Click2Drug contains a comprehensive list of computer-aided drug design (CADD) software, databases and web services. These tools are classified according to their application field, trying to cover the whole drug design pipeline". |
7157 |
| DRUG DESIGN APPS FOR SMART PHONE |
A wonderful site that harbors a number of drug designing applications for smart mobiles. |
3161 |
| Computational Resources for Drug Discove |
"CRDD (Computational Resources for Drug Discovery) is an important module of the in silico module of OSDD. The CRDD web portal provides computer resources related to drug discovery on a single platform. Following are major features of CRDD". |
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