Transcription Element Search Software (TESS)     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.

Verbumculus Genetic Sequence Analyzer     www.cs.ucr.edu/~stelo/Verbumculus An interesting tool to discover and visualize over- or under-represented words in genetic sequences. Requires Java support in browser. Also available as a downloadable program.

Advanced Genetics Wizard  www.geneticswizard.com Online program that calculates the distribution of offspring genotypes from dominant, codominant and recessive gene crosses, for up to 6 genes.

Bacterial Identification  pbil.univ-lyon1.fr/bibi/query.php Service for the identification of bacteria and fungi sequences by sequence alignment.

BiNCO-wiki  pgrc-35.ipk-gatersleben.de/pls/htmldb_pgrc/f?p=160:1:3068865960025140 Provides a collection of information on data sources for biological networks, file formats that save biological networks and software to analyze the information of these sources.

BIOBASE  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.

BioGRID  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.

BioModels Database  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.

BioMolecular Engineering Research Center  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.

Biomolecular Interaction Network Database (BIND)  bind.ca BIND is a database designed to store full descriptions of interactions, molecular complexes and pathways.

Bioverse  bioverse.compbio.washington.edu Provides a framework for exploring the relationships among the molecular, genomic, proteomic, systems, and organismal worlds.

Broad Institute: Software  www.broad.mit.edu/science/software/software Scientists at the Broad Institute have developed a range of software tools for the analysis of increasingly large genome-related datasets. These are openly available to the scientific community.

Canadian Bioinformatics Help Desk  gchelpdesk.ualberta.ca We provide bioinformatics support, services, servers, and software to Canadian researchers.

Carnac  bioinfo.lifl.fr/carnac A free software tool for analysing the hypothetical secondary structure of a family of homologous RNA.

Center for Biological Sequence Analysis  www.cbs.dtu.dk/services Offers more than 30 online services for DNA and protein bioinformatics analysis.

Center Structural Biology: Programs and Tools  www.csb.yale.edu User guides and worked examples for software applications in structural and molecular biology - from Yale Univ.

CUBIC: Columbia University Bioinformatics Center  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.

DBD: Transcription Factor Prediction Database  dbd.mrc-lmb.cam.ac.uk DBD is a database of predicted transcription factors in completely sequenced genomes. The predicted transcription factors all contain assignments to sequence specific DNA-binding domain families.

Docking Server  www.dockingserver.com Provides an internet service that calculates the site, geometry and energy of small molecules interacting with proteins.

Entrez Browser  www.ncbi.nlm.nih.gov/Entrez Retrieves molecular biology data and bibliographic citations from the NCBI's integrated databases.

ERGO  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.

Functional Human Gene Network  www.genenetwork.nl Consolidates evidence for gene-gene interactions from HPRD, BIND, Reactome, KEGG, GO, microarray co-expression and Y2H experiments. Beautiful site design.

Gene and Protein Synonyms DataBase  biomint.pharmadm.com Free service for retrieving all synonyms for a given gene or protein name.

Gene Expression Data Analysis  bioinformatics.upmc.edu/GE2/GEDA.html Normalization tests for differentially expressed genes, clustering, bootstrapping, leave-one-out validation, cross-fold validation.

Gene2MeSH  gene2mesh.ncibi.org Web application that searches gene symbols or MeSH terms and displays resulting pairs of genes and MeSH terms that match the search term.

GenePattern  www.genepattern.org This platform provides over 100 methods for the analysis and visualization of gene expression, copy number, proteomic and other data. It enables biologists to add new analyses and create workflows that can be shared, edited and published.

Genepop on the Web  wbiomed.curtin.edu.au/genepop Online version of the program for populational genetics.

Geneva Bioinformatics (GeneBio) S.A.  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.

GenOuest Bioinformatics Platform  genouest.org Provides a complete set of bioinformatics tools and public databanks updated daily, and a range of links to seminars, training courses and platform news.

gp2fasta  gp2fasta.ovh.org Converts gp files from NCBI GenPept format to fasta. Its main purpose is to create fasta files with short, but still accurate headers for sequence.

IBM Bioinformatics Group - Tools & Content  cbcsrv.watson.ibm.com/Tspd.html Several genomics and proteomics tools, including multiple alignments, gene expression analysis, tandem repeat and motif discovery.

iHOP  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.

INCBI Irish National Centre for BioInformatics  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

Informatics Tools in PubMed  into.kobic.re.kr The PubMed search system provides access to the MEDLINE and PREMEDLINE databases.

Information Génomique et Structurale (CNRS)  igs-server.cnrs-mrs.fr Online services including T-Coffee, El-Nemo, Casper and FeeBack.

InstaSeq  bioinformatics.georgetown.edu/InstaSeq.htm Google-based search engine for DNA, RNA or Protein sequences.

JustBio: Online Tool Set  www.justbio.com/tools.php A Suite of Online tools for analysis of DNA/RNA, Proteins, and Arrays.

Ligand-Gated Ion Channel Database  www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php LGICdb is a curated repository of genes coding for subunits of Ligand-Gated Ion Channels.

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.

Metab2MeSH  metab2mesh.ncibi.org Web application that searches biological substances or MeSH terms and displays resulting pairs of substances and MeSH terms that match the search term.

Michigan Molecular Interactions  mimi.ncibi.org/MimiWeb/main-page.jsp MiMi Web provides an interface to a NCIBI data repository for conducting systems biology analyses. This repository includes the MiMI database, PubMed resources updated nightly, and text mined from biomedical research sources.

Mobyle  mobyle.pasteur.fr Framework and web portal specifically designed for the integration of bioinformatics software and databanks. Provides a tutorial and an interactive guided tour.

Molecular Informatics Resource for the Analysis of Gene Expression  www.ifti.org Information methodologies, tools, and technologies relating to the study of gene expression and signal transduction from the Institute for Transcriptional Informatics.

Molecular Interactions Database (MINT)  cbm.bio.uniroma2.it/mint MINT is a database designed to store functional interactions between biological molecules (proteins, RNA, DNA).

Mulan  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.

My Genomics Resource Centre  www.mgrc.com.my A Malaysian Genomics toolset for high-throughput analysis of biological data. Must register to use.

NIH BioInformatics and Molecular Analysis Section  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.

PANDORA  www.pandora.cs.huji.ac.il Protein ANnotation Diagram ORiented Analysis service that extracts biological information from user supplied sequences.

ParAlign  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.

PathCase: Pathways Database System  nashua.case.edu/pathwaysweb An integrated software system for storing, managing, analyzing, and querying metabolic pathways at genetic, molecular, biochemical and organism levels.

PEDANT  pedant.gsf.de Completely automatic and exhaustive analysis of protein sequence sets - from individual sequences to complete genomes

PIR-International Protein Sequence Database  pir.georgetown.edu Produces a non-redundant annotated protein sequence database. PIR features integrated annotation search to support functional/structural genomics and proteomic research.

PlasMapper  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.

ProPred-I  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.

ProteinLounge  www.proteinlounge.com Bioinformatics portal which integrates protein information and many databases and research tools useful for researchers and students. Subscription based service.

PubCrawler  pubcrawler.gen.tcd.ie An online service for periodically performing predefined searches at NCBI, reporting new results by email or on the web.

QGRS Mapper  bioinformatics.ramapo.edu/QGRS Generates information on composition and distribution of putative Quadruplex forming G-Rich Sequences (QGRS) in nucleotide sequences and NCBI genes.

QualTrace DNA Sequencing  www.nucleics.com/qualtrace-dna-sequencing-demo A free online version of the QualTrace DNA sequencing software for quality control analysis of ABI 3730 and 3730xl traces files.

ReadSeq  bimas.dcrt.nih.gov/molbio/readseq Converts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others.

SA National Bioinformatics Institute  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.

Scansite  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.

Searching GenBank  www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html Text and similarity searching, provided by the National Center for Biotechnology Information (NCBI).

Sequence Analysis (Bielefeld University Bioinformatics Server)  bibiserv.techfak.uni-bielefeld.de/intro/seqdept.html Collection of sequence analysis tools.

Silva: Comprehensive Ribosomal RNA Databases  www.arb-silva.de The provided databases comprise SSU and LSU sequences of all three domains. Online search and alignment tools are available and the results can be exported in ARB and FASTA format.

Splice Center  www.tigerteamconsulting.com/SpliceCenter/SpliceOverview.jsp Suite of user-friendly tools that evaluate the impact of gene splicing variation on specific molecular biology techniques.

Splice Miner  www.tigerteamconsulting.com/SpliceMiner/intro.jsp Tool for querying Evidence Viewer Database (EVDB), a comprehensive, non-redundant collection of splice variant data for human genes.

Systems Biology of Photosynthesis  www.e-photosynthesis.org Open web platform for modeling and reverse engineering of photosynthetic dynamism.

TFM Explorer  bioinfo.lifl.fr/TFM-Explorer Scans sequences for potential Transcription Factor binding sites using Patser and TRANSFAC.

Transterm  uther.otago.ac.nz/Transterm.html 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.

UEA Plant sRNA Toolkit  srna-tools.cmp.uea.ac.uk A suite of tools for the analysis of sRNA datasets from high-throughput sequencing experiments.

WebACT  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.

YMF - DNA Motif Finding Program  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.

Your Lab Data  www.yourlabdata.com A free web-based Laboratory Information Management System (LIMS), aimed at a typical small molecular biology laboratory allowing members to have their own private forum, events, Electronic Lab Notebook (ELN) and a LIMS area.

Zinc Finger Tools  www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php Helps users design zinc finger transcription factors.