Nucleotide BLAST databases
genbank - the "classic", or taxonomic divisions of genbank (bacterial, environmental, invertebrate, other_mammalian, patent, plant, primate, rodent, STS, unannotated, viral, other_vertebrate, and gb_new - the nightly cumulative update division). This BLAST database is rebuilt nightly to include the NCBI daily update to GenBank.
genbank_htg - actually, this BLAST database includes both the High Throughput Genome (htg) and High Throughput cDNA (htc) divisions. This BLAST database is rebuilt bi-monthly with each new full release of GenBank.
genbank_notags - a BLAST set that combines the contents for genbank and genbank_htg. This BLAST database is rebuilt nightly to include the NCBI daily update to GenBank.
genbank _est - the Expressed Sequence Tags division. This BLAST database is rebuilt bi-monthly with each new full release of GenBank.
genbank_gss - the Genome Survey sequence division. This BLAST database is rebuilt bi-monthly with each new full release of GenBank.
genbank_tags - a BLAST set that combines the contents of genbank_est and genbank_gss. This BLAST database is rebuilt bi-monthly with each new full release of GenBank.
wgs - the NCBI Whole Genome Shotgun sequence division. This BLAST database is rebuilt weekly to include any updates to the wgs portion of the GenBank tree. The wgs division is maintained by ACHS as a BLAST database only. This division of GenBank consists primarily of unanotated, low pass genome sequence (see the 2006 Database issue of Nucleic Acids Research for details on the structure of GenBank).
hsapiens - the NCBI human genome construct. This BLAST database is rebuilt when significant changes are announced to the genome build.
mmusculus - the NCBI mouse genome construct. This BLAST database is rebuilt when significant changes are announced to the genome build.
yeast_genome - the NCBI yeast genome data set. This BLAST database is rebuilt when significant changes are announced to the genome build.
celegans - the C. elegans genome sequence. This BLAST database is rebuilt when significant changes are announced to the genome build.
drerio - the Zebra fish genome sequence. This BLAST database is rebuilt when significant changes are announced to the genome build.
ehistol - the E. histolitica genome. This BLAST database is rebuilt when significant changes are announced to the genome build.
Peptide BLAST databases
genpept - the translations of all ORFs in GenBank. This BLAST database is rebuilt nightly to include the NCBI daily update to GenBank.
refseqprotein - NCBI's protein reference sequence database. This BLAST database is rebuilt nightly to include the NCBI daily update to GenBank.
uniprot - the unified protein database. This BLAST database is rebuilt weekly to include the Uniprot weekly update.
swissprot - a legacy copy of the final independent release of SwissProt (ver. 44.2, of January, 2005). No longer updated
PIR - a legacy copy of the final release of Georgetown University's Protein Information Resource (ver. 80, of January, 2005). No longer updated
hs_pep - translations of the NCBI human genome. This BLAST database is rebuilt when significant changes are announced to the genome build.
mm_pep - translations of the NCBI mouse genome. This BLAST database is rebuilt when significant changes are announced to the genome build.
dr_pep - translations of the NCBI Zebra fish genome. This BLAST database is rebuilt when significant changes are announced to the genome build.
Please email comments or suggestions about the ACHS MolBiol pages to mblack@virginia.edu.
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