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Entrez Browser - http://www.ncbi.nlm.nih.gov/Entrez/
Retrieves molecular biology data and bibliographic citations from the NCBI's integrated databases. |
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PubCrawler - http://pubcrawler.gen.tcd.ie/
An online service for periodically performing predefined searches at NCBI, reporting new results by email or on the web. |
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Searching GenBank - http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html
Text and similarity searching, provided by the National Center for Biotechnology Information (NCBI). |
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PIR-International Protein Sequence Database - http://pir.georgetown.edu
Produces a non-redundant annotated protein sequence database. PIR features integrated annotation search to support functional/structural genomics and proteomic research. |
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Geneva Bioinformatics (GeneBio) S.A. - http://www.genebio.com/
GeneBio provides proteomics software tools and databases including SWISS-PROT, PROSITE, SWISS-2DPAGE and Melanie. We also offer a secure version of ExPASy molecular biology web server. |
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Biomolecular Interaction Network Database (BIND) - http://bind.ca
BIND is a database designed to store full descriptions of interactions, molecular complexes and pathways. |
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Center Structural Biology: Programs and Tools - http://www.csb.yale.edu
User guides and worked examples for software applications in structural and molecular biology - from Yale Univ. |
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Center for Biological Sequence Analysis - http://www.cbs.dtu.dk/services/
Offers more than 30 online services for DNA and protein bioinformatics analysis. |
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SA National Bioinformatics Institute - http://www.sanbi.ac.za/
SANBI aims to bring genome information, computational biology, and analytical tools to the South African research community. Hosts SA National EMBNet Node, provides links to Sequence Retrieval System (SRS), GeneKraal, and TB Genomes Analysis Server. Research in Sequence Tag Alignment and Consensus Knowledgebase (STACK). Databases include BLAST search in Mycobacterium genome. |
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BioModels Database - http://www.ebi.ac.uk/biomodels/
Resource for storing, searching and retrieving published mathematical models of biological interests. Models present in BioModels Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. |
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BioGRID - http://www.thebiogrid.org/
Database of genetic and physical interactions. It contains interaction data from many sources, including several genome/proteome-wide studies, the MIPS database, and BIND. |
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BIOBASE - http://www.gene-regulation.com/
The focus of the GBF project "Molecular Bioinformatics of Gene Regulation" are regulatory genomic signals and regions that govern transcriptional control based on TRANSFAC - The Transcription Factor Database. It compiles data about gene regulatory DNA sequences and protein factors binding to and acting through them. |
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BioMolecular Engineering Research Center - http://bmerc-www.bu.edu/index.html
Tools and methods for computational biology. Working on secondary protein structure prediction, providing reliable profiles, and developing new ways to study molecular biology through bioinformatics. |
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Ligand-Gated Ion Channel Database - http://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php
LGICdb is a curated repository of genes coding for subunits of Ligand-Gated Ion Channels. |
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Molecular Interactions Database (MINT) - http://cbm.bio.uniroma2.it/mint/
MINT is a database designed to store functional interactions between biological molecules (proteins, RNA, DNA). |
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CUBIC: Columbia University Bioinformatics Center - http://cubic.bioc.columbia.edu/
Features PredictProtein service for sequence analysis and protein structure prediction, META for single-page interface to validated sequence analysis, PredictNLS for prediction and analysis of nuclear localization signals, EVA for evaluation of automatic protein structure prediction servers, and DSSPcont for continuous assignment of protein secondary structure. |
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INCBI Irish National Centre for BioInformatics - http://acer.gen.tcd.ie/
Hosts Irish embnet node, Gives links to Database browsing and interrogation at SRS, European (EBI) servers, Blast server for parasite genomes (EBI), US (NCBI) servers, Protein structure prediction, PredictProtein Server in Heidelberg, Gene identification, splice sites, exons, introns and a list of gene structure prediction programs |
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MedMiner - http://discover.nci.nih.gov/textmining/main.jsp
An Internet biomedical data-mining tool for organizing search information gathered from textual or genetic databases - from the NIH National Cancer Inst. |
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Information Génomique et Structurale (CNRS) - http://igs-server.cnrs-mrs.fr
Online services including T-Coffee, El-Nemo, Casper and FeeBack. |
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Mulan - http://mulan.dcode.org/
Performs single-coverage local multiple DNA sequence alignments of finished and draft-quality genome sequences. It also provides with an option to predict transcription factor binding sites evolutionarily conserved across multiple species. |
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Bioverse - http://bioverse.compbio.washington.edu
Provides a framework for exploring the relationships among the molecular, genomic, proteomic, systems, and organismal worlds. |
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Scansite - http://scansite.mit.edu/
Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains. |
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IBM Bioinformatics Group - Tools & Content - http://cbcsrv.watson.ibm.com/Tspd.html
Several genomics and proteomics tools, including multiple alignments, gene expression analysis, tandem repeat and motif discovery. |
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My Genomics Resource Centre - http://www.mgrc.com.my
A Malaysian Genomics toolset for high-throughput analysis of biological data. Must register to use. |
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ParAlign - http://www.paralign.org/
Service using the ParAlign algorithm to compare genetic sequences. Apparently it is as fast as BLAST and as sensitive as Smith-Waterman. |
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Transcription Element Search Software (TESS) - http://www.cbil.upenn.edu/cgi-bin/tess/tess
Very helpful software for locating and displaying transcription factor binding sites within DNA sequences - from the Univ. of Penn. |
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Transterm - a database of mRNA regions and motifs - http://uther.otago.ac.nz/Transterm.html
Transterm - an interactive database of mRNA regions and motifs from all species and genomes. Users can browse the pre-computed data tables, search the sequence databases or search their own sequences. |
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PEDANT - http://pedant.gsf.de/
Completely automatic and exhaustive analysis of protein sequence sets - from individual sequences to complete genomes |
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NIH BioInformatics and Molecular Analysis Section - http://bimas.dcrt.nih.gov
Numerous computational tools and resources to unite advances in biology with those in computers, informatics, and networking for the genomic and genetic analysis fields of BioInformatics; division of the Computational Bioscience and Engineering Lab at the Center for Information Technology. |
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ProPred-I - http://www.imtech.res.in/raghava/propred1
An online service for predicting MHC binding regions in antigens. It also offers the proteasomal and immunoproteasomal filters to improve the applicability of results. |
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ReadSeq - http://bimas.dcrt.nih.gov/molbio/readseq/
Converts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others. |
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TFM Explorer - http://bioinfo.lifl.fr/TFM-Explorer/
Scans sequences for potential Transcription Factor binding sites using Patser and TRANSFAC. |
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Web Services at Institute of Microbial Technology, Chandigarh, India - http://imtech.res.in/raghava/www.html
Protein structure prediction (Protein Structural Classes, Secondary Structure Prediction), immunological methods (ProPred), genomics and proteomics (Genome Wise Sequence Similarity Search, Spectral Repeat Finder, 2D Gel Comparison, protein coding gene by Fast Fourier Transform), and biological databases. |
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PlasMapper - http://wishart.biology.ualberta.ca/PlasMapper/index.html
Online service to generate annotated plasmid maps up to 20 kbp. Outputs in PNG, JPG, SVG or SVGZ format. |
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iHOP - http://www.ihop-net.org/UniPub/iHOP/
Uses the network of genes and proteins as a natural way of accessing the millions of biomedical abstracts in PubMed. |
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PANDORA - http://www.pandora.cs.huji.ac.il
Protein ANnotation Diagram ORiented Analysis service that extracts biological information from user supplied sequences. |
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ProCKSI: Similarity Comparison of Proteins using Contact Maps - http://www.procksi.net
A meta-server and decision support system for Protein Comparison, Knowledge, Similarity and Information, using protein contact maps. |
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Molecular Informatics Resource for the Analysis of Gene Expression - http://www.ifti.org/
Information methodologies, tools, and technologies relating to the study of gene expression and signal transduction from the Institute for Transcriptional Informatics. |
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Canadian Bioinformatics Help Desk - http://gchelpdesk.ualberta.ca
We provide bioinformatics support, services, servers, and software to Canadian researchers. |
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WebACT - http://www.webact.org
A database of sequence comparisons between all publicly available prokaryotic genome sequences, allowing the on-line visualisation of comparisons between up to five genomic sequences, using the Artemis Comparison Tool. User can perform their comparisons on their own data. |
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LongTrace DNA Sequencing Service - https://www.nucleics.com/longtrace/
A commercial service for improving the read length and quality of ABI 3730, 3130 and 3100 DNA sequencing traces. Works via reprocessing of the raw peak data before re-base calling. A free trial is provided. |
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Advanced Genetics Wizard - http://www.geneticswizard.com
Online program that calculates the distribution of offspring genotypes from dominant, codominant and recessive gene crosses, for up to 6 genes. |
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Zinc Finger Tools - http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php
Helps users design zinc finger transcription factors. |
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YMF - DNA Motif Finding Program - http://abstract.cs.washington.edu/~saurabh/YMFWeb/YMFInput.pl
Finds novel transcription factor binding sites by searching for over-represented (most significant motifs) motifs in DNA sequences. |
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QualTrace DNA Sequencing - http://www.nucleics.com/qualtrace-dna-sequencing-demo/index.php
A free online version of the QualTrace DNA sequencing software for quality control analysis of ABI 3730 and 3730xl traces files. |
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Carnac - http://bioinfo.lifl.fr/carnac/
A free software tool for analysing the hypothetical secondary structure of a family of homologous RNA. |
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Sequence Analysis (Bielefeld University Bioinformatics Server) - http://bibiserv.techfak.uni-bielefeld.de/intro/seqdept.html
Collection of sequence analysis tools. |
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Functional Human Gene Network - http://www.genenetwork.nl
Consolidates evidence for gene-gene interactions from HPRD, BIND, Reactome, KEGG, GO, microarray co-expression and Y2H experiments. Beautiful site design. |
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ERGO - http://ergo.integratedgenomics.com/ERGO/
Online service integrating biological data from genomics, biochemistry, genetics and high-throughput expression profiling, to achieve a pattern-based analysis of genes and genomes. |
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Simulation programs for teaching population dynamics - http://www.dpw.wageningen-ur.nl/cwe/popeco/index.htm
Offers a number of educational programs including LESLIE, LOGIST, CHAOS, CELLS, WITCOM, PRED and LEWONTIN. |