Table 1

A key to the databases mentioned in this article

Database

URL

Description

COGs

http://www.ncbi.nlm.nih.gov/COG/

Clusters of orthologous groups of proteins, generated from the

comparison of protein sequences encoded in 34 complete genomes,

representing 26 major phylogenetic lineages.

DAS

http://stein.cshl.org/das/

A distributed sequence annotation system software client and

database server for the annotation of protein sequences.

Ensembl

http://www.ensembl.org/

Software for the automatic annotation of eukaryotic genomes.

Annotation and searching with gene, SNP, and cross-genome

comparative information.

EuGenes

http://iubio.bio.indiana.edu:8089/

Automatic annotations of sequence databases with gene and genomic

information, including chromosome, genetic and molecular maps.

Gene Ontology

http://www.geneontology.org/

A dynamic, controlled vocabulary applicable to the annotation of

eukaryotic genomes. Includes knowledge of the role of genes and

proteins within cells.

GeneCards

http://bioinformatics.weizmann.ac.il/cards

A database of human genes that maps genes, proteins and

diseases. Provides information on gene function.

InterPro

http://www.ebi.ac.uk/interpro/

Proteome analysis database based on Pfam, SMART, Prosite, PRINTS

and ProDom protein and domain family databases and the SWISS-

PROT and TrEMBL sequence databases. Also contains software for

the annotation of protein sequences using these databases.

LocusLink

http://www.ncbi.nlm.nih.gov/LocusLink

Interface to a database of sequence and descriptive information

correlated with genetic loci.

Mammalian

http://www.informatics.jax.org/menus/homology_menu.shtml

Mammalian homology and comparative maps. Tools and databases

Homology

from the Jackson Laboratory for the comparison of mammalian

genomes.

Pfam

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

Protein families database containing multiple sequence alignments

and hidden Markov models.

PRINTS

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

Database of protein fingerprints based on protein motifs.

ProDom

http://www.toulouse.inra.fr/prodom.html

Protein domain database based on an automatic compilation of

homologous domains.

Prosite

http://www.isrec.isb-sib.ch/profile/

Prosite profiles are protein domain profiles constructed from multiple

sequence alignments of proteins from families of related sequences.

SMART

http://smart.embl-heidelberg.de/

Protein domain families database containing multiple sequence

alignments and hidden Markov models, based on a smaller set of

domains than Pfam but designed to find domains that are more

difficult to detect.

SMD

http://genome-www4.stanford.edu/MicroArray/SMD

The Stanford microarray database of raw and normalized data from

microarray experiments, including interfaces for data retrieval and

analysis.

SWISS-PROT

http://www.expasy.ch/sprot

Protein sequence databases. SWISS-PROT represents a 'gold

and Trembl

standard' of annotation.

TIGRFAMs

http://www.tigr.org/TIGRFAMs/

Database of protein families based on hidden Markov models of

multiple protein sequence alignments.

Ponting and Dickens Genome Biology 2001 2:comment2006.1   doi:10.1186/gb-2001-2-7-comment2006