Notes on database names and nicknames for use in GCG

The databases we maintain on site for use with GCG may be referenced in several ways. Some of the most-used terms and synonyms are listed here. Note that this organization is not identical to what you will find using BLAST and other tools at the NCBI web site (for example, ACHS does not have a division equivalent to NCBI's "nr" division.

GenBank - the complete release of GenBank consists of several divisions.

genbankplus, gbp, gbplus, genembl - refers to the complete GenBank release, including the daily cumulative update

genbank, gb - refers to the complete release without the EST, GSS and HTG divisions

individual sections:

bacterial, bacteria, ba

plant, pl

primate, pr

invertebrate, in

other_mammalian, om - refers to non-Rodent and non-Primate mammalian sequences

other_vertebrate, ov - refers to non-Mammalian vertebrates

patent, pat

phage, ph

rodent, ro

sts - refers to Sequence Tagged Sites, or short genomic landmark sequences

synthetic, sy

unannotated, un

viral, vi

gb_new - refers to the cumulative (daily) update

genbank_notags, gb_notags - refers to all above divisions plus the HTG division (but without the EST and GSS divisions)

htg - refers to the HTG (High Throughput Genomic sequence) division

tags, gb_tags - refers to the combined EST and GSS divisions

est - refers to the EST (Expressed Sequence Tags) division of genbank

gss - refers to the GSS(Genome Sequence Survey) division of genbank

GenPept - this database consists of all translated coding entries from GenBank

genpept, gp - refers to the complete GenPept release, including the daily cumulative update

individual sections

gp_bacterial

gp_invertebrate

gp_other_mammalian

gp_other_vertebrate

gp_patent

gp_phage

gp_plant

gp_primate

gp_rodent

gp_synthetic

gp_unannotated

gp_viral

gp_sts

gp_new

PIR protein database (deprecated - use uniprot for current peptide data)

pir, nbrf - refers to the complete PIR release, which is updated quarterly

3d - refers to the sequence structure protein database

Swiss-Prot protein database (deprecated - use uniprot for current peptide data)

swiss-prot, swiss - refers to the complete Swiss-Prot release, which is updated weekly

C. elegans genomic database

celegans, c_elegans, worm_genome - refers to the complete nematode genome (6 chromosomes)

Yeast - genomic databases for Saccharomyces cerevisiae

yeast_orf - refers to the database of open reading frames

yeast_gb - refers to the database of GenBank entries from the yeast genome

yeastpep_nr - refers to the non-redundant peptide entries from Swiss-Prot, PIR, and GenPept

yeast_chr - refers to the complete yeast genome database (16 chromosomes plus mtDNA), annotated by chromosome number

yeast - refers to the original genome (DNA) database released in 1998

yeastpep - refers to the original protein database released in 1998

Please email comments or suggestions about the ACHS MolBiol pages to mblack@virginia.edu.

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