Biowulf High Performance Computing at the NIH
Scientific Databases

Blast_v4

Old Blast v4 databases. No longer updated at NCBI, will be deleted in summer 2020 from Biowulf.
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Database Location on HPC systemsLast Updated
16S Microbial
16S Microbial nucleotide Sequences
/fdb/blastdb/v4/16SMicrobial 15 Dec 2019
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Drosophila
Drosophila nucleotide sequences
/fdb/blastdb/v4/drosoph.nt 27 Dec 2017
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Drosophila
Drosophila protein sequences
/fdb/blastdb/v4/drosoph.aa 27 Dec 2017
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
EST - human
Human (nucleotide) sequences from the EST division of Genbank
/fdb/blastdb/v4/est_human 16 Aug 2019
(Updated weekly )
Source: ftp.ncbi.nlm.nih.gov
EST - mouse
Mouse sequences from the EST division of Genbank.
/fdb/blastdb/v4/est_mouse 16 Aug 2019
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
EST - others
Non-human, non-mouse nucleotide sequences from the EST division of Genbank
/fdb/blastdb/v4/est_others 04 Dec 2018
(Updated weekly )
Source: ftp.ncbi.nlm.nih.gov
HTGs
High throughput genome sequences
/fdb/blastdb/v4/htgs 08 Nov 2019
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Mito
Mitochondrial protein sequences
/fdb/blastdb/v4/mito.aa 16 Oct 2018
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
NCBI nr
NCBI's nonredundant Genbank CDS translations + PDB + SwissProt
/fdb/blastdb/v4/nr 10 Feb 2020
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
NCBI nt
All GenBank+EMBL+DDBJ (but no EST, STS, GSS, HTG) nucleotide sequences. No longer nonredundant.
/fdb/blastdb/v4/nt 29 Jan 2020
(Updated weekly )
Source: ftp.ncbi.nlm.nih.gov
Patent proteins
Protein sequences from patents as supplied by USPTO. Entries in this database are EXCLUDED from NCBI nr.
/fdb/blastdb/v4/pataa
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Protein Data Bank
Protein sequences of experimentally determined 3D structures of biological macromolecules. More information at the PDB.
/fdb/blastdb/v4/pdbaa 13 Dec 2019
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Protein Data Bank
Nucleotide sequences of experimentally determined 3D structures of biological macromolecules. More information at the PDB.
/fdb/blastdb/v5/pdbnt 14 Oct 2019
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
SwissProt
A highly-annotated, curated protein sequence database. Minimal redundancy and high level of integration with other databases. More information at Expasy
/fdb/blastdb/v4/swissprot 13 Dec 2019
(Updated weekly )
Source: ftp.ncbi.nlm.nih.gov
Yeast
Yeast nucleotide sequences
/fdb/blastdb/v4/yeast.nt 27 Dec 2017
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Yeast
Yeast protein sequences
/fdb/blastdb/v4/yeast.aa 27 Dec 2017
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov

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