Scientific Databases
Fasta
Fasta-format flatfile databases used by Fasta, Blat and other programs.| Database | Location on HPC systems | Last 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 | 27 Nov 2018 |
(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/ | 05 Nov 2018 |
(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 | 11 Dec 2018 |
(Updated weekly) Source: ftp.ncbi.nlm.nih.gov Mito | Mitochondrial protein sequences /fdb/fastadb/mito.aa.fas | 11 Dec 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 | 11 Dec 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 | 11 Dec 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 | 11 Dec 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 | 11 Dec 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 | 11 Dec 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 |