Catalyzing Inquiry at the Interface of Computing and Biology

ON THE NATURE OF BIOLOGICAL DATA 41

TABLE 3.1 Examples of Key Database Resources in Bioinformatics

Category Databases and URLs

Comprehensive data NCBI (National Center for Biotechnology and Information):
center: broad content http://www.ncbi.nlm.nih.gov/
including sequence,
structure, function, etc. EBI (European Bioinformatics Institute): http://www.ebi.ac.uk/

European Molecular Biology Laboratory (EMBL):

http://www.emblheidelberg.de/

TIGR (the Institute of Genome Research): http://www.tigr.org/

Whitehead/Massachusetts Institute of Technology Genome Center:

http://www-genome.wi.mit.edu/

DNA or protein sequence GenBank: http://www.ncbi.nlm.nih.gov/Genbank

DDBJ (DNA Data Bank of Japan): http://www.ddbj.nig.acjp/

EMBL Nucleotide Sequence Databank:

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

PIR (Protein Information Resource): http://pir.georgetown.edu/

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

Biomolecular interactions BIND (Biomolecular Interaction Network Database):
http://www.blueprint.org/bind/bind.php
The contents of BIND include high-throughput data submissions and
hand-curated information gathered from the scientific literature.

Genomes: complete Entrez complete genomes:
genome sequences and http://www.ncbi.nlm.nih.gov/Entrez/Genome/org.html
related information for
specific organisms Complete genome at EBI: http://www.ebi.ac.uk/genomes/

University of California, Santa Cruz, Human Genome Working Draft:

http://genome.ucsc.edu/

MGD (Mouse Genome Database): http://www.informaticsjax.org/

SGD (Saccharomyces Genome Database):

http://genomewww.stanford.edu/Saccharomyces/

FlyBase (a database of the Drosophila genome):

http://flybase.bio.indiana.edu/

WormBase (the genome and biology of Caenorhabditis elegans):

http://www.wormbase.org/

Genetics: gene mapping, GDB (Genome Database): http://gdbwww.gdb.org/gdb/
mutations, and diseases

OMIM (Online Mendelian Inheritance in Man):

http://www3.ncbi.nlm.nih.gov/Omim/searchomim.html

HGMD (Human Gene Mutation Database):

http://archive.uwcm.ac.uk/uwcm/mg/hgmdO.html

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