Genomics: A Global Resource
http://science.bio.org/

Human Genome Project
http://www.ornl.gov/hgmis/

Molecular Biologist Toolkit
http://healthlinks.washington.edu/basic_sciences/molbio/

Molecular Biology Info & Search Engines
http://restools.sdsc.edu/biotools/biotools20.html

National Biotechnology Information Facility (NBIF)
http://www.nbif.org/

The National Center for Biotechnology Information (NCBI)
http://www.ncbi.nlm.nih.gov/

The National Human Genome Research Institute (NHGRI)
http://www.nhgri.nih.gov/

UK Human Genome Mapping Project Resource Centre (HGMP-RC)
http://www.hgmp.mrc.ac.uk/

Research Collaboratory for Structural Bioinformatics (RCSB)
http://www.rcsb.org/index.html

The Sanger Centre
http://www.sanger.ac.uk/

Cell and Molecular Biology Online: An Informational Resource for Cell and Molecular Biologists
http://www.cellbio.com/index.html

Scientific Societies and Organizations

Bioinformatics Organization (Bioinformatics.Org): The Open-Access Institute
http://bioinformatics.org/

EMBnet is a science-based group of collaborating nodes throughout Europe and a number of nodes outside Europe
http://www.embnet.org/

UCSC Center for Biomolecular Science and Engineering
http://www.cbse.ucsc.edu/

Laurence H. Baker Center for Bioinformatics and Biological Statistics at Iowa State University
http://www.bioinformatics.iastate.edu/

Swiss Institute of Bioinformatics
http://en.wikipedia.org/wiki/Swiss_Institute_of_Bioinformatics

European Molecular Biology Laboratory
http://www.embl.org/

Genetic Information Research Institute
http://www.girinst.org/

Open Bioinformatics Foundation: umbrella non-profit organization supporting certain open-source projects in bioinformatics
http://www.open-bio.org/

National Center for Biomedical Ontology
http://ncbo.us

US Department of Energy Joint Genome Institute
http://www.jgi.doe.gov/

Molecular Biology Databases

MEDLINE - PubMed
http://www.ncbi.nlm.nih.gov/PubMed/

PubMed Central
http://www.pubmedcentral.nih.gov/

Taxonomic Databases 

Nucleotide Databases  

GenBank
http://www.ncbi.nlm.nih.gov/Genbank/

EMBL_Bank
http://www.ebi.ac.uk/embl/index.html

Genomic Databases  

Ensembl
http://www.ebi.ac.uk/ensembl/index.html

Entrez Genomes
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome

Protein databases 

Swiss-Prot
http://www.expasy.ch/sprot/

TrEMBL
http://www.ebi.ac.uk/trembl/

PIR
http://pir.georgetown.edu/

UniProt
http://www.ebi.ac.uk/uniprot/index.html

Secondary Protein Sequence Databases 

PRINTS
http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/

Pfam
http://www.sanger.ac.uk/Pfam/

ProDom 
http://protein.toulouse.inra.fr/prodom/current/html/home.php

InterPro
http://www.ebi.ac.uk/interpro/index.html

Structure databases 

NDB
http://ndbserver.rutgers.edu/

PQS
http://pqs.ebi.ac.uk

CCDC
http://www.ccdc.cam.ac.uk/

BioMagResBank
http://www.bmrb.wisc.edu/

Protein Structure Classification Databases 

CATH
http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html

Specialized Databases 

SGD: Saccharomyces Genome Database
http://genome-www.stanford.edu/Saccharomyces/

Human Genome Sequencing
http://www.ncbi.nlm.nih.gov/genome/seq/

GDB: Genome Database (human mapping information)
http://gdbwww.gdb.org/

MGD: Mouse Genome Database
http://www.informatics.jax.org/

Sequence Categories or Function 

Vector Database
http://seq.yeastgenome.org/vectordb/

Data Generated by Specific Sequencing Technologies 

GSS: Genome Survey Sequences
http://www.ncbi.nlm.nih.gov/dbGSS/

STS: Sequence Tagged Sites
http://www.ncbi.nlm.nih.gov/dbSTS/

HTG: High Throughput Sequences
http://www.ncbi.nlm.nih.gov/HTGS/

Information retrieval systems 

SRS (The Sequence Retrieval System)
http://srs.ebi.ac.uk/

Information Hubs for Databases and Software Tools 

ExPASy Life Science Directory
http://us.expasy.org/alinks.html

Biocatalog
http://www.ebi.ac.uk/biocat/

DBCAT
http://www.infobiogen.fr/services/dbcat/

Bio NetBook
http://www.pasteur.fr/recherche/BNB/bnb-en.html

BioHunt
http://ca.expasy.org/BioHunt/

BioWareDB
http://www.biowaredb.org/

MetaBasis
http://metabasis.bioacademy.gr/

Annual Nucleic Acids Research,  Database Issue (2006 Datababase Issue)
http://nar.oxfordjournals.org/content/vol34/suppl_1/index.dtl

Annual Nucleic Acids Research,  Web Server Issue (2005 Web Server Issue)
http://nar.oxfordjournals.org/content/vol33/suppl_2/index.dtl

NCBI BLAST
http://www.ncbi.nlm.nih.gov/BLAST

WU-BLAST
http://blast.wustl.edu

Fasta
http://www.ebi.ac.uk/fasta33/

Fasta
http://www.ebi.ac.uk/fasta/

ClustalW
http://www.ebi.ac.uk/clustalw/

DIALIGN
http://bibiserv.techfak.uni-bielefeld.de/dialign/ 

PHYLIP ( PHYLogeny Inference Package)
http://evolution.genetics.washington.edu/phylip.html

PAUP* ( Phylogenetic Analysis Using Parsimony)
http://paup.csit.fsu.edu/

RasMol
http://www.umass.edu/microbio/rasmol/

Cn3D ("See in 3-D")
http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

MolMol
http://www.mol.biol.ethz.ch/wuthrich/software/molmol/

VMD
http://www.ks.uiuc.edu/Research/vmd/

MolScript
http://www.avatar.se/molscript/

DeepView - Swiss-PdbViewer
http://www.expasy.ch/spdbv/mainpage.html

MAGE
http://kinemage.biochem.duke.edu/

TOPS
http://www3.ebi.ac.uk/tops/

GRASP
http://trantor.bioc.columbia.edu/grasp/

LIGPLOT
http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html

PyMol
http://pymol.sourceforge.net/

DALI (Distance Matrix Alignment)
http://www.ebi.ac.uk/dali/

CE (Combinatorial Extension)
http://cl.sdsc.edu/ce.html

SSAP (Sequential Structure Alignment Program)
http://www.biochem.ucl.ac.uk/~orengo/ssap.html

STRUCTAL
http://bioinfo.mbb.yale.edu/Align/server.cgi

VAST (Vector Alignment Search Tool)
http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.html

LOCK2
http://brutlag.stanford.edu/lock2/

SWISSMODEL
http://www.expasy.ch/swissmod/SWISS-MODEL.html

WHATIF
http://swift.cmbi.kun.nl/WIWWWI//

COMPOSER under SYBYL 
http://www.tripos.com

MODELLER
http://salilab.org/modeller/modeller.html

123D
http://123d.ncifcrf.gov/123D+.html

UCLA-DOE Structure Prediction Server 
http://fold.doe-mbi.ucla.edu/

NCBI Threading Package 
http://ncbi.nih.gov/Structure/RESEARCH/threading.shtml

PROSPECT
http://compbio.ornl.gov/structure/prospect2/

THREADER
http://bioinf.cs.ucl.ac.uk/threader/

3D-PSSM
http://www.sbg.bio.ic.ac.uk/%7E3dpssm/

PROCHECK
http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html

WHAT IF
http://www.cmbi.kun.nl/whatif

WHATCHEC
http://www.cmbi.kun.nl/gv/whatcheck

PROVE
http://www.ucmb.ulb.ac.be/SCMBB/PROVE

SQUID
http://www.ysbl.york.ac.uk/~oldfield/squid/

PDBsum (precomputed quality criteria)
http://www.biochem.ucl.ac.uk/bsm/pdbsum

MGED (Microarray Gene Expression Data) Society
http://www.mged.org/index.html

ArrayNorm
http://genome.tugraz.at/

Arrayplot
http://www.transcriptome.ens.fr/arrayplot/

BRB ArrayTools
http://linus.nci.nih.gov/BRB-ArrayTools.html

ChromoViz
http://www.snubi.org/software/ChromoViz/

Clinical GeneOrganizer (CGO)
http://lambertlab.uams.edu

Cluster
http://rana.lbl.gov/downloads/Cluster/Cluster_vers_2.11.zip

Clusterv
http://homes.dsi.unimi.it/~valenti/SW/clusterv/download/clusterv_1.0.tar.gz

DNMAD
http://dnmad.bioinfo.cnio.es/

Doelan
http://www.transcriptome.ens.fr/doelan/

Expression Profiler
http://www.ebi.ac.uk/expressionprofiler/

GAAS
http://www.medinfopoli.polimi.it/GAAS/

GEMS
http://genomics10.bu.edu/terrence/gems/

GeneX-Lite
http://www.ncgr.org/genex/

GEPAS
http://gepas.bioinfo.cnio.es/cgi-bin/preprocess

GMEP
http://rana.lbl.gov/downloads/gmep/

goCluster
http://www.biozentrum.unibas.ch/gocluster/

GoSurfer
http://bioinfor.bioen.uiuc.edu/gosurfer/

GRANK
http://www.bio.vu.nl/microb/research/GS4/index.html

M@CBETH
http://tomcatbackup.esat.kuleuven.be/MACBETH/index.jsp

matrix2png
http://microarray.cpmc.columbia.edu/cgibin/matrix2png.cgi

MeSHer
http://biocomp.dfci.harvard.edu/mesher.html

MGraph
http://folk.uio.no/junbaiw/mgraph/mgraph.html

MIAMExpress
http://www.ebi.ac.uk/miamexpress/

MicroArrayExplorer
http://maexplorer.sourceforge.net/

MILVA
http://www.ncrg.aston.ac.uk/Projects/milva/

NIA Array Analysis
http://lgsun.grc.nia.nih.gov/ANOVA/

NOMAD
http://ucsf-nomad.sourceforge.net/

Prism
http://noble.gs.washington.edu/prism/

ROSO
http://pbil.univlyon1.fr/roso/

ScanAlyze
http://rana.lbl.gov/downloads/ScanAlyze/ScanAlyze2_vers_2_51.exe

Simpleaffy
http://www.bioconductor.org/

SNOMAD
http://pevsnerlab.kennedykrieger.org/snomad.php

The Gene Expression Data Simulation Project
http://bioinformatics.upmc.edu/GE2/index.html

TIGR SpotFinder
http://www.tm4.org/spotfinder.html

TreeView
http://rana.lbl.gov/downloads/TreeView/TreeView_vers_1_60.exe

VARAN
http://www.bionet.espci.fr/varan/