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» Transcription Element Search Software (TESS)  
Very helpful software for locating and displaying transcription factor binding sites within DNA sequences - from the Univ. of Penn.
http://www.cbil.upenn.edu/cgi-bin/tess/tess
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» Verbumculus Genetic Sequence Analyzer
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.
http://www.cs.ucr.edu/~stelo/Verbumculus/
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» Advanced Genetics Wizard
Online program that calculates the distribution of offspring genotypes from dominant, codominant and recessive gene crosses, for up to 6 genes.
http://www.geneticswizard.com
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» BIOBASE
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 regulato
http://www.gene-regulation.com/
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» Bacterial Identification
Service for the identification of bacteria and fungi sequences by sequence alignment.
http://pbil.univ-lyon1.fr/bibi/query.php
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» BioGRID
Database of genetic and physical interactions. It contains interaction data from many sources, including several genome/proteome-wide studies, the MIPS database, and BIND.
http://www.thebiogrid.org/
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» BioModels Database
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, cont
http://www.ebi.ac.uk/biomodels/
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» BioMolecular Engineering Research Center
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.
http://bmerc-www.bu.edu/index.html
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» Bioverse
Provides a framework for exploring the relationships among the molecular, genomic, proteomic, systems, and organismal worlds.
http://bioverse.compbio.washington.edu
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» CUBIC: Columbia University Bioinformatics Center
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
http://cubic.bioc.columbia.edu/
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» Carnac
A free software tool for analysing the hypothetical secondary structure of a family of homologous RNA.
http://bioinfo.lifl.fr/carnac/
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» 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.
http://ergo.integratedgenomics.com/ERGO/
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» Entrez Browser
Retrieves molecular biology data and bibliographic citations from the NCBI's integrated databases.
http://www.ncbi.nlm.nih.gov/Entrez/
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» Functional Human Gene Network
Consolidates evidence for gene-gene interactions from HPRD, BIND, Reactome, KEGG, GO, microarray co-expression and Y2H experiments. Beautiful site design.
http://www.genenetwork.nl
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» Gene Expression Data Analysis
Normalization tests for differentially expressed genes, clustering, bootstrapping, leave-one-out validation, cross-fold validation.
http://bioinformatics.upmc.edu/GE2/GEDA.html
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» Genepop on the Web
Online version of the program for populational genetics.
http://wbiomed.curtin.edu.au/genepop/
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» Geneva Bioinformatics (GeneBio) S.A.
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.
http://www.genebio.com/
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» IBM Bioinformatics Group - Tools & Content
Several genomics and proteomics tools, including multiple alignments, gene expression analysis, tandem repeat and motif discovery.
http://cbcsrv.watson.ibm.com/Tspd.html
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» INCBI Irish National Centre for BioInformatics
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,
http://acer.gen.tcd.ie/
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» InstaSeq
Google-based search engine for DNA, RNA or Protein sequences.
http://bioinformatics.georgetown.edu/InstaSeq.htm
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» JustBio: Online Tool Set
A Suite of Online tools for analysis of DNA/RNA, Proteins, and Arrays.
http://www.justbio.com/tools.php
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» Ligand-Gated Ion Channel Database
LGICdb is a curated repository of genes coding for subunits of Ligand-Gated Ion Channels.
http://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php
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» LongTrace DNA Sequencing Service
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.
https://www.nucleics.com/longtrace/
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» MedMiner
An Internet biomedical data-mining tool for organizing search information gathered from textual or genetic databases - from the NIH National Cancer Inst.
http://discover.nci.nih.gov/textmining/main.jsp
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» Mulan
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.
http://mulan.dcode.org/
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» My Genomics Resource Centre
A Malaysian Genomics toolset for high-throughput analysis of biological data. Must register to use.
http://www.mgrc.com.my
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» NIH BioInformatics and Molecular Analysis Section
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
http://bimas.dcrt.nih.gov
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» PANDORA
Protein ANnotation Diagram ORiented Analysis service that extracts biological information from user supplied sequences.
http://www.pandora.cs.huji.ac.il
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» PEDANT
Completely automatic and exhaustive analysis of protein sequence sets - from individual sequences to complete genomes
http://pedant.gsf.de/
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» PIR-International Protein Sequence Database
Produces a non-redundant annotated protein sequence database. PIR features integrated annotation search to support functional/structural genomics and proteomic research.
http://pir.georgetown.edu
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» ParAlign
Service using the ParAlign algorithm to compare genetic sequences. Apparently it is as fast as BLAST and as sensitive as Smith-Waterman.
http://www.paralign.org/
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» PlasMapper
Online service to generate annotated plasmid maps up to 20 kbp. Outputs in PNG, JPG, SVG or SVGZ format.
http://wishart.biology.ualberta.ca/PlasMapper/index.html
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» ProPred-I
An online service for predicting MHC binding regions in antigens. It also offers the proteasomal and immunoproteasomal filters to improve the applicability of results.
http://www.imtech.res.in/raghava/propred1
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» ProteinLounge
Bioinformatics portal which integrates protein information and many databases and research tools useful for researchers and students. Subscription based service.
http://www.proteinlounge.com
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» PubCrawler
An online service for periodically performing predefined searches at NCBI, reporting new results by email or on the web.
http://pubcrawler.gen.tcd.ie/
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» QGRS Mapper
Generates information on composition and distribution of putative Quadruplex forming G-Rich Sequences (QGRS) in nucleotide sequences and NCBI genes.
http://bioinformatics.ramapo.edu/QGRS/
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» QualTrace DNA Sequencing
A free online version of the QualTrace DNA sequencing software for quality control analysis of ABI 3730 and 3730xl traces files.
http://www.nucleics.com/qualtrace-dna-sequencing-demo/index.php
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» ReadSeq
Converts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others.
http://bimas.dcrt.nih.gov/molbio/readseq/
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» SA National Bioinformatics Institute
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. Resea
http://www.sanbi.ac.za/
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» Scansite
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.
http://scansite.mit.edu/
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» Searching GenBank
Text and similarity searching, provided by the National Center for Biotechnology Information (NCBI).
http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html
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» TFM Explorer
Scans sequences for potential Transcription Factor binding sites using Patser and TRANSFAC.
http://bioinfo.lifl.fr/TFM-Explorer/
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» Transterm - a database of mRNA regions and motifs
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.
http://uther.otago.ac.nz/Transterm.html
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» Web Services at Institute of Microbial Technology, Chandigarh, India
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
http://imtech.res.in/raghava/www.html
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» WebACT
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 o
http://www.webact.org
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» YMF - DNA Motif Finding Program
Finds novel transcription factor binding sites by searching for over-represented (most significant motifs) motifs in DNA sequences.
http://abstract.cs.washington.edu/~saurabh/YMFWeb/YMFInput.pl
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» Zinc Finger Tools
Helps users design zinc finger transcription factors.
http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php
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» iHOP
Uses the network of genes and proteins as a natural way of accessing the millions of biomedical abstracts in PubMed.
http://www.ihop-net.org/UniPub/iHOP/
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