Biowulf High Performance Computing at the NIH
Scientific Databases

Blast

Blast v5 databases. For use via command-line Blast or easyblast on Biowulf
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Database Location on HPC systemsLast Updated
Betacoronavirus
Blast v5 database: Betacoronavirus nucleotide sequence data
/fdb/blastdb/Betacoronavirus 06 May 2020
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Human Genome GRCh38.p13
Genome Reference Consortium Human Build 38 Patch Release 13 (2019/02/28).
/fdb/blastdb/GRCh38.p13 12 Feb 2020
(Updated one-time)
Source: ftp.ncbi.nlm.nih.gov
Human Genome GRCh38.p13 proteins
Genome Reference Consortium Human Build 38 Patch Release 13 (2019/02/28) proteins
/fdb/blastdb/GRCh38.p13.prot 12 Feb 2020
(Updated one-time)
Source: ftp.ncbi.nlm.nih.gov
IMGT
The IMGT reference directory in FASTA format is constituted by sets of immunoglobulin (IG) or T cell receptor (TR) sequences which are isolated from the IMGT reference sequences from IMGT/GENE-DB. By definition, the IMGT reference directory sets contain one sequence for each allele. Allele names of these sequences are shown in red in Alignments of alleles. In the V-REGION and C-GENE exon sets, IMGT gaps have been introduced according to the IMGT unique numbering [1] [2] [3] [4]. Gene names with provisional nomenclature (with a letter S) correspond to genes not yet assigned to genomic mapped genes. They correspond to insertion/deletion polymorphism in different strains or to mutated genes. NL: Not Localized. IMGT reference sequence and gene orientation: An IMGT reference sequence for a given IG or TR gene in the IMGT reference directory in FASTA format (IMGT/GENE-DB, IMGT/V-QUEST) is provided in the 5' > 3' DNA strand orientation corresponding to the 'sense', 'plus' or 'coding strand' of that gene (DNA strand orientation). The orientation (direct or opposite) of an IG or TR gene in a given IMGT locus is given in Locus Gene order (Genomic orientation) IMGT Repertoire (IG and TR) > 1. Locus and genes > 3. Locus descriptions > Locus gene order
/fdb/igblast/imgt-2022
(Updated one-time)
Source: igblast mkdir -pv imgt-2022 export PATH=$PATH:
Mouse Genome (Mus Musculus) mm39
Mouse genome (mm39, Genome Reference Consortium Mouse Build 39 (GCA_000001635.9))
/fdb/blastdb/mm39 01 Jun 2021
(Updated one-time)
Source: genome-ftp.cse.ucsc.edu
Mouse Genome (Mus Musculus) mm39 Proteins
Mouse genome (mm39, Genome Reference Consortium Mouse Build 39 (GCA_000001635.9)) Proteins
/fdb/blastdb/mm39.protein 01 Jun 2021
(Updated one-time)
Source: www.ncbi.nlm.nih.gov
Mouse Genome (Mus Musculus) mm39 RNA
Mouse genome (mm39, Genome Reference Consortium Mouse Build 39 (GCA_000001635.9)) RNA sequences
/fdb/blastdb/mm39.rna 01 Jun 2021
(Updated one-time)
Source: www.ncbi.nlm.nih.gov
Mouse Genome GRCm38.p6
Genome Reference Consortium Mouse Build 38 patch release 6 (2017/09/15)
/fdb/blastdb/GRCm38.p6 12 Feb 2020
(Updated after new build release)
Source: ftp.ncbi.nlm.nih.gov
Mouse Genome GRCm38.p6 proteins
Genome Reference Consortium Mouse Build 38 patch release 6 (2017/09/15) proteins
/fdb/blastdb/GRCm38.p6.prot 12 Feb 2020
(Updated after release)
Source: ftp.ncbi.nlm.nih.gov
NCBI nr
NCBI nr protein v5 database for Blast 2.8.0+ onwards
/fdb/blastdb/nr 04 Mar 2020
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
NCBI nt
NCBI nucleotide nt v5 Blast database for Blast 2.8.0+ onwards
/fdb/blastdb/nt 03 Mar 2020
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Protein Data Bank
Blast 5 database: Protein sequences of experimentally determined 3D structures of biological macromolecules. More information at the PDB.
/fdb/blastdb/pdbaa 04 Mar 2020
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Protein Data Bank
Blast v5 database: Nucleotide sequences of experimentally determined 3D structures of biological macromolecules. More information at the PDB.
/fdb/blastdb/pdbnt 07 Dec 2019
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
SwissProt
Swissprot Blast v5 database for Blast 2.8.0+ onwards
/fdb/blastdb/swissprot 04 Mar 2020
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov

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