Database | Type | Available formats | Location on the Helix Systems | Accessible via | Last updated |
1000 Genomes 20100804 release containing analysis results sets (vcfs) and README files. |
Nuc | vcf files | /fdb/1000genomes/ | 19 Dec 2012 (Updated occasionally | |
Cambridge Structural Database Crystal structure information for over 165,000 organic and organometallic compounds. More info at CCDC. |
3-D | CSD | /local/csd | Quest | 16 Jan 2013 (Updated every 3 months |
Chicken Genome May 2006 assembly from WUSTL. |
Nuc | MySQL | NIH mirror of UCSC Genome Browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
25 Jan 2013 (Updated weekly |
Prot | MySQL | NIH mirror of UCSC Genome Browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
25 Jan 2013 (Updated weekly | |
Annotations | MySQL | NIH mirror of UCSC Genome Browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
25 Jan 2013 (Updated weekly | |
Cow Genome Aug 2006 assembly from the Baylor Sequencing Center |
Nuc | MySQL | NIH mirror of UCSC genome browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
31 Jan 2012 (Updated weekly |
Prot | MySQL | NIH mirror of UCSC genome browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
31 Jan 2012 (Updated weekly | |
Annotations | MySQL | NIH mirror of UCSC genome browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
31 Jan 2012 (Updated weekly | |
Dog Genome May 2005 assembly from the Broad Institute |
Nuc | MySQL | NIH mirror of UCSC genome browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
25 Jan 2013 (Updated weekly |
Prot | MySQL | NIH mirror of UCSC genome browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
25 Jan 2013 (Updated weekly | |
Annotations | MySQL | NIH mirror of UCSC genome browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
25 Jan 2013 (Updated weekly | |
Drosophila Drosophila sequences |
Nuc | Blast | /fdb/blastdb/drosoph.nt | Blast (Helix)
Blast (Biowulf) |
26 Sep 2011 (Updated weekly |
Fasta | /fdb/fastadb/drosoph.nt.fas | Fasta, BLAT. User programs. | 04 Sep 2012 (Updated weekly | ||
Prot | Blast | /fdb/blastdb/drosoph.aa | Blast (Helix)
Blast (Biowulf) |
26 Sep 2011 (Updated weekly | |
Fasta | /fdb/fastadb/drosoph.aa.fas | Fasta, BLAT. User programs. | 04 Sep 2012 (Updated weekly | ||
Drosophila genome April 2006 assembly |
Annotations | MySQL | NIH mirror of UCSC genome browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
25 Jan 2013 (Updated weekly |
EST EST division of Genbank |
Nuc | EMBOSS | /fdb/embossdb/est.new | EMBOSS web
interface , EMBOSS command-line |
24 Aug 2012 (Updated bimonthly after Genbank release |
EST - human Human sequences from the EST division of Genbank |
Nuc | Blast | /fdb/blastdb/est_human | Blast (Helix)
Blast (Biowulf) |
23 May 2012 (Updated weekly |
Fasta | /fdb/fastadb/est_human.fas | Fasta, BLAT. User programs. | 12 Feb 2013 (Updated weekly | ||
EST - mouse Mouse sequences from the EST division of Genbank. |
Nuc | Blast | /fdb/blastdb/est_mouse | Blast (Helix)
Blast (Biowulf) |
23 May 2012 (Updated weekly |
Fasta | /fdb/fastadb/est_mouse.fas | Fasta, BLAT. User programs. | 12 Feb 2013 (Updated weekly | ||
EST - others Non-human, non-mouse sequences from the EST division of Genbank |
Nuc | Blast | /fdb/blastdb/est_others | Blast (Helix)
Blast (Biowulf) |
23 May 2012 (Updated weekly |
Gb_New All sequences added to Genbank since last major release |
Nuc | EMBOSS | /fdb/embossdb/gbnew.new | EMBOSS web
interface , EMBOSS command-line |
14 Feb 2013 (Updated daily |
Genbank The NIH Genetic Sequence Database, an annotated collection of all publicly available DNA sequences. More information at NCBI. |
Nuc | EMBOSS | /fdb/embossdb/genbank.new | EMBOSS web
interface , EMBOSS command-line |
19 Dec 2012 (Updated bimonthly after Genbank release |
GenPept GenPept is produced by parsing the corresponding GenBank release for translated coding regions of GenBank sequences. More information at NCI, Frederick |
Prot | EMBOSS | /fdb/embossdb/genpept.new | EMBOSS web
interface , EMBOSS command-line |
12 Dec 2012 (Updated bimonthly after Genbank release |
GP_New All sequences added to GenPept since last major release |
Prot | EMBOSS | /fdb/embossdb/gpnew.new | EMBOSS web
interface , EMBOSS command-line |
02 Oct 2012 (Updated daily |
HTGs High throughput genome sequences |
Nuc | Blast | /fdb/blastdb/htgs | Blast (Helix)
Blast (Biowulf) |
17 Aug 2012 (Updated weekly |
Human Genome hg18 Build 36, hg18 (Apr 2006) from the International Human Genome Consortium |
Nuc | Blast | /fdb/genome/human-apr2006/hs_genome | Blast (Helix)
Blast (Biowulf) |
20 May 2011 (Updated after new build release |
Fasta | /fdb/genome/human-apr2006/ | Fasta, BLAT. User programs. | 20 May 2011 (Updated after new build release | ||
MySQL | NIH mirror of UCSC Genome Browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
01 Feb 2013 (Updated weekly | ||
Prot | MySQL | NIH mirror of UCSC Genome Browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
01 Feb 2013 (Updated weekly | |
Annotations | MySQL | NIH mirror of UCSC Genome Browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
01 Feb 2013 (Updated weekly | |
Human Genome hg19 Build 37, hg19 (Feb 2009) from the International Human Genome Consortium |
Nuc | Blast | /fdb/blastdb/hs_genome | Blast (Helix)
Blast (Biowulf) |
19 Nov 2012 (Updated after new build release |
Fasta | /fdb/genome/human-feb2009/ | Fasta, BLAT. User programs. | 19 Nov 2012 (Updated after new build release | ||
MySQL | NIH mirror of UCSC Genome Browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
01 Feb 2013 (Updated weekly | ||
Prot | MySQL | NIH mirror of UCSC Genome Browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
01 Feb 2013 (Updated weekly | |
Annotations | MySQL | NIH mirror of UCSC Genome Browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
01 Feb 2013 (Updated weekly | |
Human Genome Proteins hg18 Build 36, hg18 (Apr 2006) from the International Human Genome Consortium |
Prot | Blast | /fdb/genome/human-apr2006/hs_genome.protein | Blast (Helix)
Blast (Biowulf) |
28 Apr 2006 (Updated after build release |
Blast | /fdb/genome/human-apr2006/hs_genome.protein | Blast (Helix)
Blast (Biowulf) |
28 Apr 2006 (Updated after build release | ||
Human Genome Proteins hg19 Build 37, hg19 (Feb 2009) from the International Human Genome Consortium |
Prot | Fasta | /fdb/fastadb/hs_genome.protein.fas | Fasta, BLAT. User programs. | 12 Apr 2010 (Updated after build release |
Blast | /fdb/blastdb/hs_genome.protein | Blast (Helix)
Blast (Biowulf) |
05 Nov 2012 (Updated after build release | ||
Human Genome RNA hg18 Build 36, hg18 (Apr 2006) from the International Human Genome Consortium |
Nuc | Blast | /fdb/genome/human-apr2006/hs_genome.rna | Blast (Helix)
Blast (Biowulf) |
28 Apr 2006 (Updated after build release |
Fasta | /fdb/genome/human-apr2006/hs_genome.rna.fas | Fasta, BLAT. User programs. | 28 Apr 2006 (Updated after build release | ||
Human Genome RNA hg19 Build 37, hg19 (Feb 2009) from the International Human Genome Consortium |
Nuc | Fasta | /fdb/fastadb/hs_genome.rna.fas | Fasta, BLAT. User programs. | 12 Apr 2010 (Updated after build release |
Blast | /fdb/blastdb/hs_genome.rna | Blast (Helix)
Blast (Biowulf) |
05 Nov 2012 (Updated after build release | ||
Mito Mitochondrial sequences |
Nuc | Blast | /fdb/blastdb/mito.nt | Blast (Helix)
Blast (Biowulf) |
11 Feb 2013 (Updated weekly |
Fasta | /fdb/fastadb/mito.nt.fas | Fasta, BLAT. User programs. | 12 Feb 2013 (Updated weekly | ||
Prot | Blast | /fdb/blastdb/mito.aa | Blast (Helix)
Blast (Biowulf) |
11 Feb 2013 (Updated weekly | |
Fasta | /fdb/fastadb/mito.aa.fas | Fasta, BLAT. User programs. | 12 Feb 2013 (Updated weekly | ||
Mouse Genome mm8 Build 36, mm8, Mar 2006 from the Mouse Genome Consortium |
Nuc | Blast | /fdb/genome/mouse-mar2006/mouse_genome | Blast (Helix)
Blast (Biowulf) |
09 Nov 2006 (Updated after new build release |
Fasta | /fdb/genome/mouse-mar2006/ | Fasta, BLAT. User programs. | 08 Jul 2010 (Updated after new build release | ||
MySQL | NIH mirror of UCSC Genome Browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
01 Feb 2013 (Updated weekly | ||
Prot | MySQL | NIH mirror of UCSC Genome Browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
01 Feb 2013 (Updated weekly | |
Annotations | MySQL | NIH mirror of UCSC Genome Browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
01 Feb 2013 (Updated weekly | |
Mouse Genome mm9 Build 37, mm9, Jul 2007 from the Mouse Genome Consortium |
Nuc | Blast | /fdb/blastdb/mouse_genome | Blast (Helix)
Blast (Biowulf) |
25 Mar 2008 (Updated after new build release |
Fasta | /fdb/genome/mouse-jul2007/ | Fasta, BLAT. User programs. | 06 Apr 2011 (Updated after new build release | ||
MySQL | NIH mirror of UCSC Genome Browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
01 Feb 2013 (Updated weekly | ||
Prot | MySQL | NIH mirror of UCSC Genome Browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
01 Feb 2013 (Updated weekly | |
Annotations | MySQL | NIH mirror of UCSC Genome Browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
01 Feb 2013 (Updated weekly | |
Mouse Genome Proteins mm8 Build 36, mm8, Mar 2006 from the Mouse Genome Consortium |
Prot | Blast | /fdb/genome/mouse-mar2006/mouse_genome.protein | Blast (Helix)
Blast (Biowulf) |
09 Nov 2006 (Updated weekly |
Fasta | /fdb/genome/mouse-mar2006/mouse_genome.protein.fas | Fasta, BLAT. User programs. | 09 Nov 2006 (Updated weekly | ||
Mouse Genome Proteins mm9 Build 37, mm9, Jul 2007 from the Mouse Genome Consortium |
Prot | Blast | /fdb/genome/mouse-mar2006/mouse_genome.protein | Blast (Helix)
Blast (Biowulf) |
09 Nov 2006 (Updated weekly |
Fasta | /fdb/fastadb/mouse_genome.protein.fas | Fasta, BLAT. User programs. | 25 Mar 2008 (Updated weekly | ||
Mouse Genome RNA mm8 Build 36, mm8, Mar 2006 from the Mouse Genome Consortium |
Nuc | Blast | /fdb/genome/mouse-mar2006/mouse_genome.rna | Blast (Helix)
Blast (Biowulf) |
09 Nov 2006 (Updated after release |
Mouse Genome RNA mm9 Build 37, mm9, Jul 2007 from the Mouse Genome Consortium |
Nuc | Blast | /fdb/blastdb/mouse_genome.rna | Blast (Helix)
Blast (Biowulf) |
22 Oct 2012 (Updated after release |
Fasta | /fdb/fastadb/mouse_genome.rna.fas | Fasta, BLAT. User programs. | 25 Mar 2008 (Updated after release | ||
MSDB A nonredundant protein sequence database designed specifically for mass-spec applications. |
Prot | Mascot | biospec.nih.gov | Mascot search engine | 01 Jun 2010 (Updated weekly |
NCBI nr NCBI's nonredundant Genbank CDS translations + PDB + SwissProt |
Prot | Blast | /fdb/blastdb/nr | Blast (Helix)
Blast (Biowulf) |
06 Feb 2013 (Updated weekly |
Fasta | /fdb/fastadb/nr.aa.fas | Fasta, BLAT. User programs. | 12 Feb 2013 (Updated weekly | ||
Mascot | biospec.nih.gov | Mascot search engine | 10 Feb 2013 (Updated weekly | ||
NCBI nt All GenBank+EMBL+DDBJ (but no EST, STS, GSS, HTG). No longer nonredundant. |
Nuc | Blast | /fdb/blastdb/nt | Blast (Helix)
Blast (Biowulf) |
06 Feb 2013 (Updated weekly |
Fasta | /fdb/fastadb/nt.fas | Fasta, BLAT. User programs. | 12 Feb 2013 (Updated weekly | ||
NIH-Specific A collection of NIH-specific databases requested by NIH Mascot users. |
Prot | Mascot | biospec.nih.gov | Mascot search engine | 13 Feb 2013 (Updated as requested |
PFAM A collection of multiple sequence alignments and hidden Markov models. More information at PFAM home page |
Families | PFAM | /fdb/fastadb/pfam | HMMER (Biowulf, Helix) | 23 Mar 2009 (Updated every 3 months |
Prints Protein fingerprints, groups of conserved motifs used to characterize a protein family. |
Patterns | EMBOSS | used internally by Emboss | EMBOSS web
interface , EMBOSS command-line |
13 Feb 2013 (Updated after new Prints release |
Prosite A database/dictionary of protein sites and patterns. More information at Expasy. |
Patterns | EMBOSS | used internally by Emboss | EMBOSS web
interface , EMBOSS command-line |
13 Feb 2013 (Updated every 2 months |
Protein Data Bank An archive of experimentally determined three-dimensional strtures of biological macromolecules. More information at the PDB. |
Nuc | Blast | /fdb/blastdb/pdbnt | Blast (Helix)
Blast (Biowulf) |
07 Feb 2013 (Updated weekly |
Fasta | /fdb/fastadb/pdb.nt.fas | Fasta, BLAT. User programs. | 12 Feb 2013 (Updated weekly | ||
Prot | Blast | /fdb/blastdb/pdbaa | Blast (Helix)
Blast (Biowulf) |
07 Feb 2013 (Updated weekly | |
Fasta | /fdb/fastadb/pdb.aa.fas | Fasta, BLAT. User programs. | 12 Feb 2013 (Updated weekly | ||
3-D | PDB | /pdb/pdb | Molecules R Us or direct access to coordinate files. NIH users can NFS-mount the PDB databases on their own machines -- contact staff@helix.nih.gov for more info. |
14 Feb 2013 (Updated daily | |
Rat Genome May 2006 build, rn4, from the Rat Genome Sequencing Consortium |
Nuc | MySQL | NIH mirror of UCSC genome browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
25 Jan 2013 (Updated weekly |
Prot | MySQL | NIH mirror of UCSC genome browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
25 Jan 2013 (Updated weekly | |
Annotations | MySQL | NIH mirror of UCSC genome browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
25 Jan 2013 (Updated weekly | |
REBASE About restriction enzymes, recognition sequences, cleavage sites... More information at REBASE. |
Enzymes | EMBOSS | used internally by Emboss | EMBOSS web
interface , EMBOSS command-line |
13 Feb 2013 (Updated every month |
Refseq Human Genomic Refseq Human (NC_######) chromosome records with gap adjusted concatenated NT_ contigs |
Nuc | Blast | /fdb/blastdb/human_genomic | Blast (Helix)
Blast (Biowulf) |
09 Feb 2013 (Updated weekly |
Fasta | /fdb/fastadb/ref.human.genomic.fas | Fasta, BLAT. User programs. | 12 Feb 2013 (Updated weekly | ||
Refseq Human Proteins A comprehensive, integrated, non-redundant set of sequences. More info at NCBI |
Prot | Blast | /fdb/blastdb/human.protein | Blast (Helix)
Blast (Biowulf) |
11 Feb 2013 (Updated weekly |
Fasta | /fdb/fastadb/ref.human.protein.fas | Fasta, BLAT. User programs. | 12 Feb 2013 (Updated weekly | ||
Refseq Human RNA A comprehensive, integrated, non-redundant set of sequences. More info at NCBI |
Nuc | Blast | /fdb/blastdb/human.rna | Blast (Helix)
Blast (Biowulf) |
11 Feb 2013 (Updated weekly |
Fasta | /fdb/fastadb/ref.human.rna.fas | Fasta, BLAT. User programs. | 12 Feb 2013 (Updated weekly | ||
Refseq Mouse Proteins A comprehensive, integrated, non-redundant set of sequences. More info at NCBI |
Prot | Blast | /fdb/blastdb/mouse.protein | Blast (Helix)
Blast (Biowulf) |
11 Feb 2013 (Updated weekly |
Fasta | /fdb/fastadb/ref.mouse.protein.fas | Fasta, BLAT. User programs. | 12 Feb 2013 (Updated weekly | ||
Refseq Mouse RNA A comprehensive, integrated, non-redundant set of sequences. More info at NCBI |
Nuc | Blast | /fdb/blastdb/mouse.rna | Blast (Helix)
Blast (Biowulf) |
11 Feb 2013 (Updated weekly |
Fasta | /fdb/fastadb/ref.mouse.rna.fas | Fasta, BLAT. User programs. | 12 Feb 2013 (Updated weekly | ||
Refseq Other Genomic RefSeq chromosome records (NC_######) for organisms other than human |
Nuc | Blast | /fdb/blastdb/other_genomic | Blast (Helix)
Blast (Biowulf) |
06 Feb 2013 (Updated weekly |
Fasta | /fdb/fastadb/ref.other.genomic.fas | Fasta, BLAT. User programs. | 12 Feb 2013 (Updated weekly | ||
Refseqaa NCBI's comprehensive, integrated, non-redundant set of protein sequences for major research organisms. |
Prot | EMBOSS | /fdb/embossdb/refseqaa.new | EMBOSS web
interface , EMBOSS command-line |
16 Jan 2013 (Updated weekly |
Refseqnt NCBI's comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA) for major research organisms. |
Nuc | EMBOSS | /fdb/embossdb/refseqnt.new | EMBOSS web
interface , EMBOSS command-line |
16 Jan 2013 (Updated weekly |
Rhesus genome Jan 2006 assembly from the Baylor Sequencing Center. |
Nuc | MySQL | NIH mirror of UCSC genome browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
25 Jan 2013 (Updated weekly |
Prot | MySQL | NIH mirror of UCSC genome browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
25 Jan 2013 (Updated weekly | |
Annotations | MySQL | NIH mirror of UCSC genome browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
25 Jan 2013 (Updated weekly | |
Sp_Trembl SwissProt + Trembl (a computer-annotated supplement of SwissProt) |
Prot | Mascot | biospec.nih.gov | Mascot search engine | 10 Feb 2013 (Updated weekly |
SwissProt A highly-annotated, curated protein sequence database. Minimal redundancy and high level of integration with other databases. More information at Expasy |
Prot | Blast | /fdb/blastdb/swissprot | Blast (Helix)
Blast (Biowulf) |
11 Feb 2013 (Updated weekly |
Fasta | /fdb/fastadb/swissprot.aa.fas | Fasta, BLAT. User programs. | 12 Feb 2013 (Updated weekly | ||
Mascot | biospec.nih.gov | Mascot search engine | 10 Feb 2013 (Updated weekly | ||
UniProt (Swissprot + Trembl) A highly-annotated, curated protein sequence database. Minimal redundancy and high level of integration with other databases. More information at Expasy |
Prot | EMBOSS | /fdb/embossdb/uniprot | EMBOSS web
interface , EMBOSS command-line |
06 Feb 2013 (Updated weekly |
Yeast Yeast sequences |
Nuc | Blast | /fdb/blastdb/yeast.nt | Blast (Helix)
Blast (Biowulf) |
26 Sep 2011 (Updated weekly |
Fasta | /fdb/fastadb/yeast.nt.fas | Fasta, BLAT. User programs. | 04 Sep 2012 (Updated weekly | ||
Prot | Blast | /fdb/blastdb/yeast.aa | Blast (Helix)
Blast (Biowulf) |
26 Sep 2011 (Updated weekly | |
Fasta | /fdb/fastadb/yeast.aa.fas | Fasta, BLAT. User programs. | 30 Jun 2011 (Updated weekly | ||
Zebrafish genome Mar 2006 assembly from the Sanger Center. |
Nuc | MySQL | NIH mirror of UCSC genome browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
29 Nov 2011 (Updated weekly |
Prot | MySQL | NIH mirror of UCSC genome browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
29 Nov 2011 (Updated weekly | |
Annotations | MySQL | NIH mirror of UCSC genome browser | NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes. |
29 Nov 2011 (Updated weekly |