Biowulf High Performance Computing at the NIH
Scientific Databases

Fasta

Fasta-format flatfile databases used by Fasta, Blat and other programs.
Back to main database page
Database Location on HPC systemsLast Updated
Cat genome (Felis Catus) 9.0
Nov 2017 (Felis catus 9.0, felCat9) assembly from Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine.
/fdb/ensembl/pub/release-96/fasta/felis_catus =
(Updated one-time)
Source: ftp.ensembl.org
Dog Genome (Canis familiaris) 3.1
May 2011 assembly from the Broad Institute
/fdb/ensembl/pub/release-96/fasta/canis_familiaris =
(Updated one-time)
Source: ftp.ensembl.org
Drosophila
Drosophila nucleotide sequences
/fdb/fastadb/drosoph.nt.fas =
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Drosophila
Drosophila protein sequences
/fdb/fastadb/drosoph.aa.fas =
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
EST - human
Human nucleotide sequences from the EST division of Genbank.
/fdb/fastadb/est_human.fas =
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
EST - mouse
Mouse nucleotide sequences from the EST division of Genbank.
/fdb/fastadb/est_mouse.fas =
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Human Genome GRCh38
Sep 2013 assembly of human genome. See info at NCBI
/fdb/ensembl/pub/release-96/fasta/homo_sapiens =
(Updated one-time)
Source: ftp.ensembl.org
Human Genome GRCh38
GRCh38.p2 is the second patch release for the GRCh38 reference assembly from the Genome Reference Consortium. Release date December 8, 2014. More info at GRC site.
/fdb/genome/GRCh38.p2/ =
(Updated one-time)
Source: ftp.ncbi.nlm.nih.gov
Human Genome hg17
Build 35, hg17 (May 2004) from the International Human Genome Consortium
/fdb/genome/hg17/ =
(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/ =
(Updated one-time)
Source: genome-ftp.cse.ucsc.edu
Human Genome hg19
Build 37, hg19 (Feb 2009) from the International Human Genome Consortium
/fdb/genome/human-feb2009/ =
(Updated one-time)
Source: genome-ftp.cse.ucsc.edu
Human Genome Proteins hg19
Build 37, hg19 (Feb 2009) from the International Human Genome Consortium
/fdb/fastadb/hs_genome.protein.fas =
(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.fas =
(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/fastadb/hs_genome.rna.fas =
(Updated after build release)
Source: ftp.ncbi.nlm.nih.gov
Mito
Mitochondrial nucleotide sequences
/fdb/fastadb/mito.nt.fas =
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Mito
Mitochondrial protein sequences
/fdb/fastadb/mito.aa.fas =
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Mouse Genome (Mus musculus) mm10
mm10, GRC Build 38
/fdb/genome/mm10/ =
(Updated after new build release)
Source: genome-ftp.cse.ucsc.edu
Mouse Genome (Mus musculus) mm10
mm10, GRC Build 38
/fdb/ensembl/pub/release-96/fasta/mus_musculus =
(Updated one-time)
Source: ftp.ensembl.org
Mouse Genome (Mus musculus) mm8
Build 36, mm8, Mar 2006 from the Mouse Genome Consortium
/fdb/genome/mouse-mar2006/ =
(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/genome/mm9/ =
(Updated after new build release)
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.fas =
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Mouse Genome Proteins mm9
Build 37, mm9, Jul 2007 from the Mouse Genome Consortium
/fdb/fastadb/mouse_genome.protein.fas =
(Updated one-time)
Source: ftp.ncbi.nlm.nih.gov
Mouse Genome RNA mm9
Build 37, mm9, Jul 2007 from the Mouse Genome Consortium
/fdb/fastadb/mouse_genome.rna.fas =
(Updated after release)
Source: ftp.ncbi.nlm.nih.gov
NCBI nr
NCBI's nonredundant Genbank CDS translations + PDB + SwissProt
/fdb/fastadb/nr.aa.fas =
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
NCBI nt
All GenBank+EMBL+DDBJ (but no EST, STS, GSS, HTG). No longer nonredundant.
/fdb/fastadb/nt.fas =
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Protein Data Bank
An archive of experimentally determined three-dimensional strtures of biological macromolecules. More information at the PDB.
/fdb/fastadb/pdb.aa.fas =
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Protein Data Bank
An archive of experimentally determined three-dimensional strtures of biological macromolecules. More information at the PDB.
/fdb/fastadb/pdb.nt.fas =
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Rat Genome (Rattus norvegicus) rn5
March 2012 build, rn5, from the Rat Genome Sequencing Consortium
/fdb/genome/rn5 =
(Updated one-time)
Source: genome-ftp.cse.ucsc.edu
Refseq Human Genomic
Refseq Human (NC_######) chromosome records with gap adjusted concatenated NT_ contigs
/fdb/fastadb/ref.human.genomic.fas =
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Refseq Human Proteins
A comprehensive, integrated, non-redundant set of sequences. More info at NCBI
/fdb/fastadb/ref.human.protein.fas =
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Refseq Human RNA
A comprehensive, integrated, non-redundant set of sequences. More info at NCBI
/fdb/fastadb/ref.human.rna.fas =
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Refseq Mouse Proteins
A comprehensive, integrated, non-redundant set of sequences. More info at NCBI
/fdb/fastadb/ref.mouse.protein.fas =
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Refseq Mouse RNA
A comprehensive, integrated, non-redundant set of sequences. More info at NCBI
/fdb/fastadb/ref.mouse.rna.fas =
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Refseq Other Genomic
RefSeq chromosome records (NC_######) for organisms other than human
/fdb/fastadb/ref.other.genomic.fas =
(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/fastadb/swissprot.aa.fas =
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Xenopus tropicalis genome
WGS) assembly v4.1 sequenced/assembled by the DOE Joint Genome Institute (JGI).
/fdb/genome/xenTro-apr2006 =
(Updated one-time)
Source: genome.jgi-psf.org
Yeast
Yeast nucleotide sequences
/fdb/fastadb/yeast.nt.fas =
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Yeast
Yeast protein sequences
/fdb/fastadb/yeast.aa.fas =
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Zebrafish genome (Danio Rerio)
Mar 2006 assembly from the Sanger Center.
/fdb/genome/Zv10 =
(Updated one-time)
Source: ftp.ncbi.nlm.nih.gov

Back to main database page