Biowulf High Performance Computing at the NIH
Scientific Databases

Blast

formatted for the NCBI Blast program. For use via command-line Blast on HPC systems.
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Database Location on HPC systemsLast Updated
16S Microbial
16S Microbial nucleotide Sequences
/fdb/blastdb/16SMicrobial 09 Dec 2018
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Drosophila
Drosophila nucleotide sequences
/fdb/blastdb/drosoph.nt 27 Dec 2017
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Drosophila
Drosophila protein sequences
/fdb/blastdb/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/est_human 20 Nov 2018
(Updated weekly )
Source: ftp.ncbi.nlm.nih.gov
EST - mouse
Mouse sequences from the EST division of Genbank.
/fdb/blastdb/est_mouse 31 May 2016
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
EST - others
Non-human, non-mouse nucleotide sequences from the EST division of Genbank
/fdb/blastdb/est_others 04 Dec 2018
(Updated weekly )
Source: ftp.ncbi.nlm.nih.gov
HTGs
High throughput genome sequences
/fdb/blastdb/htgs 02 Oct 2018
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Human Genome hg17
Build 35, hg17 (May 2004) from the International Human Genome Consortium
/fdb/genome/hg17/ 25 Aug 2004
(Updated one-time)
Source: genome-ftp.cse.ucsc.edu
Human Genome hg18
Build 36, hg18 (Apr 2006) from the International Human Genome Consortium
/fdb/genome/hg18 31 Jan 2014
(Updated one-time)
Source: genome-ftp.cse.ucsc.edu
Human Genome hg19
Build 37, hg19 (Feb 2009) from the International Human Genome Consortium
/fdb/blastdb/hs_genome 05 Nov 2018
(Updated one-time)
Source: genome-ftp.cse.ucsc.edu
Human Genome Proteins hg18
Build 36, hg18 (Apr 2006) from the International Human Genome Consortium
/fdb/genome/human-apr2006/hs_genome.protein 28 Apr 2006
(Updated after build release)
Source: ftp.ncbi.nlm.nih.gov
Human Genome Proteins hg18
Build 36, hg18 (Apr 2006) from the International Human Genome Consortium
/fdb/genome/human-apr2006/hs_genome.protein 28 Apr 2006
(Updated after build release)
Source: ftp.ncbi.nlm.nih.gov
Human Genome Proteins hg19
Build 37, hg19 (Feb 2009) from the International Human Genome Consortium
/fdb/blastdb/hs_genome.protein 27 Jun 2016
(Updated after build release)
Source: ftp.ncbi.nlm.nih.gov
Human Genome RNA hg18
Build 36, hg18 (Apr 2006) from the International Human Genome Consortium
/fdb/genome/human-apr2006/hs_genome.rna 28 Apr 2006
(Updated after build release)
Source: ftp.ncbi.nlm.nih.gov
Human Genome RNA hg19
Build 37, hg19 (Feb 2009) from the International Human Genome Consortium
/fdb/blastdb/hs_genome.rna 27 Jun 2016
(Updated after build release)
Source: ftp.ncbi.nlm.nih.gov
Mito
Mitochondrial protein sequences
/fdb/blastdb/mito.aa 16 Oct 2018
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Mouse Genome (Mus musculus) mm10
mm10, GRC Build 38
/fdb/blastdb/mm10 25 Mar 2008
(Updated after new build release)
Source: genome-ftp.cse.ucsc.edu
Mouse Genome (Mus musculus) mm8
Build 36, mm8, Mar 2006 from the Mouse Genome Consortium
/fdb/genome/mouse-mar2006/mouse_genome 09 Nov 2006
(Updated after new build release)
Source: genome-ftp.cse.ucsc.edu
Mouse Genome (Mus musculus) mm9
Build 37, mm9, Jul 2007 from the Mouse Genome Consortium
/fdb/blastdb/mouse_genome 25 Mar 2008
(Updated one-time)
Source: genome-ftp.cse.ucsc.edu
Mouse Genome Proteins mm8
Build 36, mm8, Mar 2006 from the Mouse Genome Consortium
/fdb/genome/mouse-mar2006/mouse_genome.protein 09 Nov 2006
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Mouse Genome Proteins mm9
Build 37, mm9, Jul 2007 from the Mouse Genome Consortium
/fdb/genome/mouse-mar2006/mouse_genome.protein 09 Nov 2006
(Updated one-time)
Source: ftp.ncbi.nlm.nih.gov
Mouse Genome RNA mm8
Build 36, mm8, Mar 2006 from the Mouse Genome Consortium
/fdb/genome/mouse-mar2006/mouse_genome.rna 09 Nov 2006
(Updated after release)
Source: ftp.ncbi.nlm.nih.gov
Mouse Genome RNA mm9
Build 37, mm9, Jul 2007 from the Mouse Genome Consortium
/fdb/blastdb/mouse_genome.rna 27 Jun 2016
(Updated after release)
Source: ftp.ncbi.nlm.nih.gov
NCBI nr
NCBI's nonredundant Genbank CDS translations + PDB + SwissProt
/fdb/blastdb/nr 04 Dec 2018
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
NCBI nr
NCBI nr v5 database for Blast 2.8.0+
/fdb/blastdb/v5/nr 06 Jun 2018
(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/nt 11 Dec 2018
(Updated weekly )
Source: ftp.ncbi.nlm.nih.gov
NCBI nt
NCBI nt v5 Blast database for Blast 2.8.0+
/fdb/blastdb/v5/nt 06 Jun 2018
(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/pdbaa 12 Dec 2018
(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/pdbnt 11 Dec 2018
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Refseq Human Genomic
Refseq Human (NC_######) chromosome records with gap adjusted concatenated NT_ contigs
/fdb/blastdb/human_genomic 23 Jul 2017
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Refseq Human Proteins
A comprehensive, integrated, non-redundant set of sequences. More info at NCBI
/fdb/blastdb/human.protein 03 Nov 2014
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Refseq Human RNA
A comprehensive, integrated, non-redundant set of sequences. More info at NCBI
/fdb/blastdb/human.rna 03 Nov 2014
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Refseq Mouse Proteins
A comprehensive, integrated, non-redundant set of sequences. More info at NCBI
/fdb/blastdb/mouse.protein 03 Nov 2014
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Refseq Mouse RNA
A comprehensive, integrated, non-redundant set of sequences. More info at NCBI
/fdb/blastdb/mouse.rna 03 Nov 2014
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Refseq Other Genomic
RefSeq chromosome records (NC_######) for organisms other than human
/fdb/blastdb/other_genomic 24 Jun 2017
(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/swissprot 12 Dec 2018
(Updated weekly )
Source: ftp.ncbi.nlm.nih.gov
SwissProt
Swissprot Blast v5 database for Blast 2.8.0+
/fdb/blastdb/v5/swissprot 06 Jun 2018
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Viral
Viral nucleotide sequences from NCBI
/fdb/blastdb/viral 12 Dec 2018
(Updated weekly)
Source: Virus sequences collected from NCBInt, Refseq and Patent databases.
Viral
Viral protein sequences from NCBI
/fdb/blastdb/viral 10 Dec 2018
(Updated weekly)
Source: -
Yeast
Yeast nucleotide sequences
/fdb/blastdb/yeast.nt 27 Dec 2017
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Yeast
Yeast protein sequences
/fdb/blastdb/yeast.aa 27 Dec 2017
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov

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