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Scientific Databases

Fasta

Fasta-format flatfile databases used by Fasta, Blat and other programs.
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Database Location on HPC systemsLast Updated
Cat genome (Felis Catus) 6.2
Sep 2011 (Felis catus 6.2, felCat5) assembly by the International Cat Genome Sequencing Consortium.
/fdb/ensembl/pub/release-77/fasta/felis_catus 31 May 2016
(Updated one-time)
Source: ftp.ensembl.org
Dog Genome (Canis familiaris)
May 2005 assembly from the Broad Institute
/fdb/ensembl/pub/release-77/fasta/canis_familiaris 31 May 2016
(Updated one-time)
Source: ftp.ensembl.org
Drosophila
Drosophila nucleotide sequences
/fdb/fastadb/drosoph.nt.fas 04 Sep 2012
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Drosophila
Drosophila protein sequences
/fdb/fastadb/drosoph.aa.fas 04 Sep 2012
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
EST - human
Human nucleotide sequences from the EST division of Genbank.
/fdb/fastadb/est_human.fas 21 Mar 2017
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
EST - mouse
Mouse nucleotide sequences from the EST division of Genbank.
/fdb/fastadb/est_mouse.fas 21 Mar 2017
(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-77/fasta/homo_sapiens 31 May 2016
(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/ 13 Apr 2015
(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/ 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/genome/human-feb2009/ 24 Aug 2017
(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 12 Apr 2010
(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 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/fastadb/hs_genome.rna.fas 12 Apr 2010
(Updated after build release)
Source: ftp.ncbi.nlm.nih.gov
Mito
Mitochondrial nucleotide sequences
/fdb/fastadb/mito.nt.fas 14 Aug 2018
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Mito
Mitochondrial protein sequences
/fdb/fastadb/mito.aa.fas 14 Aug 2018
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Mouse Genome (Mus musculus) mm10
mm10, GRC Build 38
/fdb/genome/mm10/ 06 Apr 2011
(Updated after new build release)
Source: genome-ftp.cse.ucsc.edu
Mouse Genome (Mus musculus) mm10
mm10, GRC Build 38
/fdb/ensembl/pub/release-77/fasta/mus_musculus 31 May 2016
(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/ 08 Jul 2010
(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/ 06 Apr 2011
(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 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/fastadb/mouse_genome.protein.fas 25 Mar 2008
(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 25 Mar 2008
(Updated after release)
Source: ftp.ncbi.nlm.nih.gov
NCBI nr
NCBI's nonredundant Genbank CDS translations + PDB + SwissProt
/fdb/fastadb/nr.aa.fas 14 Aug 2018
(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 14 Aug 2018
(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 14 Aug 2018
(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 14 Aug 2018
(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 07 Jan 2013
(Updated one-time)
Source: genome-ftp.cse.ucsc.edu
Rat Genome (Rattus norvegicus) rn5
March 2012 build, rn5, from the Rat Genome Sequencing Consortium
/fdb/ensembl/pub/release-77/fasta/rattus_norvegicus =
(Updated one-time)
Source: ftp.ensembl.org
Refseq Human Genomic
Refseq Human (NC_######) chromosome records with gap adjusted concatenated NT_ contigs
/fdb/fastadb/ref.human.genomic.fas 25 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/fastadb/ref.human.protein.fas 04 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/fastadb/ref.human.rna.fas 04 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/fastadb/ref.mouse.protein.fas 04 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/fastadb/ref.mouse.rna.fas 04 Nov 2014
(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 24 Jul 2018
(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 14 Aug 2018
(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 15 Oct 2014
(Updated one-time)
Source: genome.jgi-psf.org
Yeast
Yeast nucleotide sequences
/fdb/fastadb/yeast.nt.fas 04 Sep 2012
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Yeast
Yeast protein sequences
/fdb/fastadb/yeast.aa.fas 30 Jun 2011
(Updated weekly)
Source: ftp.ncbi.nlm.nih.gov
Zebrafish genome (Danio Rerio)
Mar 2006 assembly from the Sanger Center.
/fdb/genome/Zv10 16 Oct 2014
(Updated one-time)
Source: ftp.ncbi.nlm.nih.gov

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