Scientific Databases
Blast
formatted for the NCBI Blast program. For use via command-line Blast on HPC systems.| Database | Location on HPC systems | Last Updated
| 16S Microbial | 16S Microbial nucleotide Sequences /fdb/blastdb/16SMicrobial | 13 Oct 2019 |
(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 | 16 Aug 2019 |
(Updated weekly ) Source: ftp.ncbi.nlm.nih.gov EST - mouse | Mouse sequences from the EST division of Genbank. /fdb/blastdb/est_mouse | 16 Aug 2019 |
(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 | 03 Oct 2019 |
(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 | 26 Sep 2019 |
(Updated weekly) Source: ftp.ncbi.nlm.nih.gov NCBI nr | NCBI nr v5 database for Blast 2.8.0+ /fdb/blastdb/v5/nr | (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 | 03 Oct 2019 |
(Updated weekly ) Source: ftp.ncbi.nlm.nih.gov NCBI nt | NCBI nt v5 Blast database for Blast 2.8.0+ /fdb/blastdb/v5/nt | (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 | 09 Oct 2019 |
(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 | 09 Oct 2019 |
(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 | 09 Oct 2019 |
(Updated weekly ) Source: ftp.ncbi.nlm.nih.gov SwissProt | Swissprot Blast v5 database for Blast 2.8.0+ /fdb/blastdb/v5/swissprot | (Updated weekly) Source: ftp.ncbi.nlm.nih.gov Viral | Viral nucleotide sequences from NCBI /fdb/blastdb/viral | (Updated weekly) Source: Virus sequences collected from NCBInt, Refseq and Patent databases. Viral | Viral protein sequences from NCBI /fdb/blastdb/viral | 04 Mar 2019 |
(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 |