Web Directory

» 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

» 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 regulatory DNA seq
   http://www.gene-regulation.com/

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

» BiNCO-wiki
   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.
   http://pgrc-35.ipk-gatersleben.de/pls/htmldb_pgrc/f?p=160:1:3068865960025140

» 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/

» 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/

» 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

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

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

» Broad Institute: 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.
   http://www.broad.mit.edu/science/software/software

» 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/

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

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

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

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

» DBD: Transcription Factor Prediction Database
   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.
   http://dbd.mrc-lmb.cam.ac.uk

» Docking Server
   Provides an internet service that calculates the site, geometry and energy of small molecules interacting with proteins.
   http://www.dockingserver.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.
   http://ergo.integratedgenomics.com/ERGO/

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

» 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

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

» 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

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

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

» GenePattern
   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.
   http://www.genepattern.org

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

» 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/

» 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

» 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/

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

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

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

» 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

» 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/

» Malaysian Genomics Resource Centre Berhad
   MGRC provides contract genomes services, sequencing services and data and access tools.
   http://www.mgrc.com.my

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

» Michigan Molecular Interactions
   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.
   http://mimi.ncibi.org/MimiWeb/main-page.jsp

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

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

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

» 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/

» 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

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

» 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/

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

» 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/

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

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

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

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

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

» Transterm
   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

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

» 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

» 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

» Your Lab Data
   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.
   http://www.yourlabdata.com/

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

» gp2fasta
   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.
   http://gp2fasta.ovh.org/

» 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/