Scientific Databases

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Database	Type	Location on the Helix Systems	Last Updated
EMBOSS databases Accessible via See: EMBOSS web interface EMBOSS command-line
EST EST division of Genbank	Nuc	/fdb/embossdb/est.new	18 Apr 2013 (Updated bimonthly after Genbank release Source:NCBI )
Gb_New All sequences added to Genbank since last major release	Nuc	/fdb/embossdb/gbnew.new	23 May 2013 (Updated daily Source:NCBI )
Genbank The NIH Genetic Sequence Database, an annotated collection of all publicly available DNA sequences. More information at NCBI.	Nuc	/fdb/embossdb/genbank.new	17 Apr 2013 (Updated bimonthly after Genbank release Source:NCBI )
Refseqnt NCBI's comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA) for major research organisms.	Nuc	/fdb/embossdb/refseqnt.new	08 May 2013 (Updated weekly Source:NCBI)
Prints Protein fingerprints, groups of conserved motifs used to characterize a protein family.	Patterns	used internally by Emboss	22 Apr 2013 (Updated after new Prints release Source:EBI)
Prosite A database/dictionary of protein sites and patterns. More information at Expasy.	Patterns	used internally by Emboss	15 May 2013 (Updated every 2 months Source:Expasy )
REBASE About restriction enzymes, recognition sequences, cleavage sites... More information at REBASE.	Enzymes	used internally by Emboss	22 May 2013 (Updated every month Source:REBASE )
GenPept GenPept is produced by parsing the corresponding GenBank release for translated coding regions of GenBank sequences. More information at NCI, Frederick	Prot	/fdb/embossdb/genpept.new	12 Dec 2012 (Updated bimonthly after Genbank release Source:NCIFCRF)
GP_New All sequences added to GenPept since last major release	Prot	/fdb/embossdb/gpnew.new	02 Oct 2012 (Updated daily Source:NCIFCRF )
Refseqaa NCBI's comprehensive, integrated, non-redundant set of protein sequences for major research organisms.	Prot	/fdb/embossdb/refseqaa.new	08 May 2013 (Updated weekly Source:NCBI)
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	/fdb/embossdb/uniprot	01 May 2013 (Updated weekly Source:Uniprot)
Blast databases Accessible via See: Blast (Helix) Blast (Biowulf)
Drosophila Drosophila sequences	Nuc	/fdb/blastdb/drosoph.nt	26 Sep 2011 (Updated weekly Source:NCBI )
EST - human Human sequences from the EST division of Genbank	Nuc	/fdb/blastdb/est_human	23 May 2012 (Updated weekly Source:NCBI )
EST - mouse Mouse sequences from the EST division of Genbank.	Nuc	/fdb/blastdb/est_mouse	23 May 2012 (Updated weekly Source:NCBI )
EST - others Non-human, non-mouse sequences from the EST division of Genbank	Nuc	/fdb/blastdb/est_others	23 May 2012 (Updated weekly Source:NCBI )
HTGs High throughput genome sequences	Nuc	/fdb/blastdb/htgs	21 Apr 2013 (Updated weekly Source:NCBI )
Human Genome hg18 Build 36, hg18 (Apr 2006) from the International Human Genome Consortium	Nuc	/fdb/genome/human-apr2006/hs_genome	20 May 2011 (Updated after new build release Source:UCSC )
Human Genome hg19 Build 37, hg19 (Feb 2009) from the International Human Genome Consortium	Nuc	/fdb/blastdb/hs_genome	02 May 2013 (Updated after new build release Source:UCSC )
Human Genome RNA hg18 Build 36, hg18 (Apr 2006) from the International Human Genome Consortium	Nuc	/fdb/genome/human-apr2006/hs_genome.rna	28 Apr 2006 (Updated after build release Source:NCBI )
Human Genome RNA hg19 Build 37, hg19 (Feb 2009) from the International Human Genome Consortium	Nuc	/fdb/blastdb/hs_genome.rna	05 Nov 2012 (Updated after build release Source:NCBI )
Mito Mitochondrial sequences	Nuc	/fdb/blastdb/mito.nt	20 May 2013 (Updated weekly Source:NCBI )
Mouse Genome mm8 Build 36, mm8, Mar 2006 from the Mouse Genome Consortium	Nuc	/fdb/genome/mouse-mar2006/mouse_genome	09 Nov 2006 (Updated after new build release Source:UCSC )
Mouse Genome mm9 Build 37, mm9, Jul 2007 from the Mouse Genome Consortium	Nuc	/fdb/blastdb/mouse_genome	25 Mar 2008 (Updated after new build release Source:UCSC )
Mouse Genome RNA mm8 Build 36, mm8, Mar 2006 from the Mouse Genome Consortium	Nuc	/fdb/genome/mouse-mar2006/mouse_genome.rna	09 Nov 2006 (Updated after release Source:NCBI )
Mouse Genome RNA mm9 Build 37, mm9, Jul 2007 from the Mouse Genome Consortium	Nuc	/fdb/blastdb/mouse_genome.rna	22 Oct 2012 (Updated after release Source:NCBI )
NCBI nt All GenBank+EMBL+DDBJ (but no EST, STS, GSS, HTG). No longer nonredundant.	Nuc	/fdb/blastdb/nt	15 May 2013 (Updated weekly Source:NCBI )
Protein Data Bank An archive of experimentally determined three-dimensional strtures of biological macromolecules. More information at the PDB.	Nuc	/fdb/blastdb/pdbnt	16 May 2013 (Updated weekly Source:NCBI )
Refseq Human Genomic Refseq Human (NC_######) chromosome records with gap adjusted concatenated NT_ contigs	Nuc	/fdb/blastdb/human_genomic	18 May 2013 (Updated weekly Source:NCBI)
Refseq Human RNA A comprehensive, integrated, non-redundant set of sequences. More info at NCBI	Nuc	/fdb/blastdb/human.rna	20 May 2013 (Updated weekly Source:NCBI)
Refseq Mouse RNA A comprehensive, integrated, non-redundant set of sequences. More info at NCBI	Nuc	/fdb/blastdb/mouse.rna	20 May 2013 (Updated weekly Source:NCBI)
Refseq Other Genomic RefSeq chromosome records (NC_######) for organisms other than human	Nuc	/fdb/blastdb/other_genomic	28 Feb 2013 (Updated weekly Source:NCBI )
Yeast Yeast sequences	Nuc	/fdb/blastdb/yeast.nt	26 Sep 2011 (Updated weekly Source:NCBI )
Drosophila Drosophila sequences	Prot	/fdb/blastdb/drosoph.aa	26 Sep 2011 (Updated weekly Source:NCBI )
Human Genome Proteins hg18 Build 36, hg18 (Apr 2006) from the International Human Genome Consortium	Prot	/fdb/genome/human-apr2006/hs_genome.protein	28 Apr 2006 (Updated after build release Source:NCBI )
Human Genome Proteins hg18 Build 36, hg18 (Apr 2006) from the International Human Genome Consortium	Prot	/fdb/genome/human-apr2006/hs_genome.protein	28 Apr 2006 (Updated after build release Source:NCBI )
Human Genome Proteins hg19 Build 37, hg19 (Feb 2009) from the International Human Genome Consortium	Prot	/fdb/blastdb/hs_genome.protein	05 Nov 2012 (Updated after build release Source:NCBI )
Mito Mitochondrial sequences	Prot	/fdb/blastdb/mito.aa	20 May 2013 (Updated weekly Source:NCBI )
Mouse Genome Proteins mm8 Build 36, mm8, Mar 2006 from the Mouse Genome Consortium	Prot	/fdb/genome/mouse-mar2006/mouse_genome.protein	09 Nov 2006 (Updated weekly Source:NCBI )
Mouse Genome Proteins mm9 Build 37, mm9, Jul 2007 from the Mouse Genome Consortium	Prot	/fdb/genome/mouse-mar2006/mouse_genome.protein	09 Nov 2006 (Updated weekly Source:NCBI )
NCBI nr NCBI's nonredundant Genbank CDS translations + PDB + SwissProt	Prot	/fdb/blastdb/nr	25 Apr 2013 (Updated weekly Source:NCBI )
Protein Data Bank An archive of experimentally determined three-dimensional strtures of biological macromolecules. More information at the PDB.	Prot	/fdb/blastdb/pdbaa	16 May 2013 (Updated weekly Source:NCBI )
Refseq Human Proteins A comprehensive, integrated, non-redundant set of sequences. More info at NCBI	Prot	/fdb/blastdb/human.protein	20 May 2013 (Updated weekly Source:NCBI)
Refseq Mouse Proteins A comprehensive, integrated, non-redundant set of sequences. More info at NCBI	Prot	/fdb/blastdb/mouse.protein	20 May 2013 (Updated weekly Source:NCBI)
SwissProt A highly-annotated, curated protein sequence database. Minimal redundancy and high level of integration with other databases. More information at Expasy	Prot	/fdb/blastdb/swissprot	20 May 2013 (Updated weekly Source:NCBI)
Yeast Yeast sequences	Prot	/fdb/blastdb/yeast.aa	26 Sep 2011 (Updated weekly Source:NCBI )
Fasta databases Accessible via See: Fasta, BLAT.
Drosophila Drosophila sequences	Prot	/fdb/fastadb/drosoph.aa.fas	04 Sep 2012 (Updated weekly Source:NCBI )
Human Genome Proteins hg19 Build 37, hg19 (Feb 2009) from the International Human Genome Consortium	Prot	/fdb/fastadb/hs_genome.protein.fas	12 Apr 2010 (Updated after build release Source:NCBI )
Mito Mitochondrial sequences	Prot	/fdb/fastadb/mito.aa.fas	21 May 2013 (Updated weekly Source:NCBI )
Mouse Genome Proteins mm8 Build 36, mm8, Mar 2006 from the Mouse Genome Consortium	Prot	/fdb/genome/mouse-mar2006/mouse_genome.protein.fas	09 Nov 2006 (Updated weekly Source:NCBI )
Mouse Genome Proteins mm9 Build 37, mm9, Jul 2007 from the Mouse Genome Consortium	Prot	/fdb/fastadb/mouse_genome.protein.fas	25 Mar 2008 (Updated weekly Source:NCBI )
NCBI nr NCBI's nonredundant Genbank CDS translations + PDB + SwissProt	Prot	/fdb/fastadb/nr.aa.fas	21 May 2013 (Updated weekly Source:NCBI )
Protein Data Bank An archive of experimentally determined three-dimensional strtures of biological macromolecules. More information at the PDB.	Prot	/fdb/fastadb/pdb.aa.fas	21 May 2013 (Updated weekly Source:NCBI )
Refseq Human Proteins A comprehensive, integrated, non-redundant set of sequences. More info at NCBI	Prot	/fdb/fastadb/ref.human.protein.fas	21 May 2013 (Updated weekly Source:NCBI)
Refseq Mouse Proteins A comprehensive, integrated, non-redundant set of sequences. More info at NCBI	Prot	/fdb/fastadb/ref.mouse.protein.fas	21 May 2013 (Updated weekly Source:NCBI)
SwissProt A highly-annotated, curated protein sequence database. Minimal redundancy and high level of integration with other databases. More information at Expasy	Prot	/fdb/fastadb/swissprot.aa.fas	21 May 2013 (Updated weekly Source:NCBI )
Yeast Yeast sequences	Prot	/fdb/fastadb/yeast.aa.fas	30 Jun 2011 (Updated weekly Source:NCBI )
Drosophila Drosophila sequences	Nuc	/fdb/fastadb/drosoph.nt.fas	04 Sep 2012 (Updated weekly Source:NCBI )
EST - human Human sequences from the EST division of Genbank.	Nuc	/fdb/fastadb/est_human.fas	21 May 2013 (Updated weekly Source:NCBI )
EST - mouse Mouse sequences from the EST division of Genbank.	Nuc	/fdb/fastadb/est_mouse.fas	21 May 2013 (Updated weekly Source:NCBI )
Human Genome hg18 Build 36, hg18 (Apr 2006) from the International Human Genome Consortium	Nuc	/fdb/genome/human-apr2006/	20 May 2011 (Updated after new build release Source:UCSC)
Human Genome hg19 Build 37, hg19 (Feb 2009) from the International Human Genome Consortium	Nuc	/fdb/genome/human-feb2009/	02 May 2013 (Updated after new build release Source:UCSC)
Human Genome RNA hg18 Build 36, hg18 (Apr 2006) from the International Human Genome Consortium	Nuc	/fdb/genome/human-apr2006/hs_genome.rna.fas	28 Apr 2006 (Updated after build release Source:NCBI )
Human Genome RNA hg19 Build 37, hg19 (Feb 2009) from the International Human Genome Consortium	Nuc	/fdb/fastadb/hs_genome.rna.fas	12 Apr 2010 (Updated after build release Source:NCBI )
Mito Mitochondrial sequences	Nuc	/fdb/fastadb/mito.nt.fas	21 May 2013 (Updated weekly Source:NCBI )
Mouse Genome mm8 Build 36, mm8, Mar 2006 from the Mouse Genome Consortium	Nuc	/fdb/genome/mouse-mar2006/	08 Jul 2010 (Updated after new build release Source:UCSC )
Mouse Genome mm9 Build 37, mm9, Jul 2007 from the Mouse Genome Consortium	Nuc	/fdb/genome/mouse-jul2007/	06 Apr 2011 (Updated after new build release Source:UCSC )
Mouse Genome RNA mm9 Build 37, mm9, Jul 2007 from the Mouse Genome Consortium	Nuc	/fdb/fastadb/mouse_genome.rna.fas	25 Mar 2008 (Updated after release Source:NCBI )
NCBI nt All GenBank+EMBL+DDBJ (but no EST, STS, GSS, HTG). No longer nonredundant.	Nuc	/fdb/fastadb/nt.fas	21 May 2013 (Updated weekly Source:NCBI )
Protein Data Bank An archive of experimentally determined three-dimensional strtures of biological macromolecules. More information at the PDB.	Nuc	/fdb/fastadb/pdb.nt.fas	21 May 2013 (Updated weekly Source:NCBI )
Refseq Human Genomic Refseq Human (NC_######) chromosome records with gap adjusted concatenated NT_ contigs	Nuc	/fdb/fastadb/ref.human.genomic.fas	21 May 2013 (Updated weekly Source:NCBI)
Refseq Human RNA A comprehensive, integrated, non-redundant set of sequences. More info at NCBI	Nuc	/fdb/fastadb/ref.human.rna.fas	21 May 2013 (Updated weekly Source:NCBI)
Refseq Mouse RNA A comprehensive, integrated, non-redundant set of sequences. More info at NCBI	Nuc	/fdb/fastadb/ref.mouse.rna.fas	21 May 2013 (Updated weekly Source:NCBI)
Refseq Other Genomic RefSeq chromosome records (NC_######) for organisms other than human	Nuc	/fdb/fastadb/ref.other.genomic.fas	21 May 2013 (Updated weekly Source:NCBI)
Yeast Yeast sequences	Nuc	/fdb/fastadb/yeast.nt.fas	04 Sep 2012 (Updated weekly Source:NCBI )
Mascot databases Accessible via Mascot search engine
MSDB A nonredundant protein sequence database designed specifically for mass-spec applications.	Prot	biospec.nih.gov	01 Jun 2010 (Updated weekly Source:NCBI )
NCBI nr NCBI's nonredundant Genbank CDS translations + PDB + SwissProt	Prot	biospec.nih.gov	19 May 2013 (Updated weekly Source:NCBI )
NIH-Specific A collection of NIH-specific databases requested by NIH Mascot users.	Prot	biospec.nih.gov	15 May 2013 (Updated as requested Source:NIH)
Sp_Trembl SwissProt + Trembl (a computer-annotated supplement of SwissProt)	Prot	biospec.nih.gov	05 May 2013 (Updated weekly Source:Expasy )
SwissProt A highly-annotated, curated protein sequence database. Minimal redundancy and high level of integration with other databases. More information at Expasy	Prot	biospec.nih.gov	05 May 2013 (Updated weekly Source:Expasy )
PDB databases Accessible via 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.
Protein Data Bank An archive of experimentally determined three-dimensional strtures of biological macromolecules. More information at the PDB.	3-D	/pdb/pdb	24 May 2013 (Updated daily Source:PDB )
CSD databases Accessible via Quest
Cambridge Structural Database Crystal structure information for over 165,000 organic and organometallic compounds. More info at CCDC.	3-D	/local/csd	16 Jan 2013 (Updated every 3 months Source:CCDC)
PFAM databases Accessible via HMMER (Biowulf, Helix)
PFAM A collection of multiple sequence alignments and hidden Markov models. More information at PFAM home page	Families	/fdb/fastadb/pfam	23 Mar 2009 (Updated every 3 months Source:PFAM )
MySQL databases Accessible via Also available for direct MySQL queries from the Biowulf cluster nodes.
Chicken Genome May 2006 assembly from WUSTL.	Nuc	NIH mirror of UCSC Genome Browser	05 Apr 2013 (Updated weekly Source:UCSC )
Cow Genome Mar 2005 assembly from the Baylor Sequencing Center	Nuc	NIH mirror of UCSC genome browser	31 Jan 2012 (Updated weekly Source:UCSC )
Dog Genome May 2005 assembly from the Broad Institute	Nuc	NIH mirror of UCSC genome browser	25 Jan 2013 (Updated weekly Source:UCSC )
Human Genome hg18 Build 36, hg18 (Apr 2006) from the International Human Genome Consortium	Nuc	NIH mirror of UCSC Genome Browser	17 May 2013 (Updated weekly Source:UCSC )
Human Genome hg19 Build 37, hg19 (Feb 2009) from the International Human Genome Consortium	Nuc	NIH mirror of UCSC Genome Browser	17 May 2013 (Updated weekly Source:UCSC )
Mouse Genome mm8 Build 36, mm8, Mar 2006 from the Mouse Genome Consortium	Nuc	NIH mirror of UCSC Genome Browser	17 May 2013 (Updated weekly Source:UCSC )
Mouse Genome mm9 Build 37, mm9, Jul 2007 from the Mouse Genome Consortium	Nuc	NIH mirror of UCSC Genome Browser	17 May 2013 (Updated weekly Source:UCSC )
Rat Genome May 2006 build, rn4, from the Rat Genome Sequencing Consortium	Nuc	NIH mirror of UCSC genome browser	10 May 2013 (Updated weekly Source:UCSC )
Rhesus genome Jan 2006 assembly from the Baylor Sequencing Center.	Nuc	NIH mirror of UCSC genome browser	25 Jan 2013 (Updated weekly Source:UCSC )
Zebrafish genome Mar 2006 assembly from the Sanger Center.	Nuc	NIH mirror of UCSC genome browser	29 Nov 2011 (Updated weekly Source:UCSC )
Chicken Genome May 2006 assembly from WUSTL.	Annotations	NIH mirror of UCSC Genome Browser	05 Apr 2013 (Updated weekly Source:UCSC )
Cow Genome Mar 2005 assembly from the Baylor Sequencing Center	Annotations	NIH mirror of UCSC genome browser	31 Jan 2012 (Updated weekly Source:UCSC )
Dog Genome May 2005 assembly from the Broad Institute	Annotations	NIH mirror of UCSC genome browser	25 Jan 2013 (Updated weekly Source:UCSC )
Drosophila genome April 2006 assembly	Annotations	NIH mirror of UCSC genome browser	10 May 2013 (Updated weekly Source:UCSC)
Human Genome hg18 Build 36, hg18 (Apr 2006) from the International Human Genome Consortium	Annotations	NIH mirror of UCSC Genome Browser	17 May 2013 (Updated weekly Source:UCSC)
Human Genome hg19 Build 37, hg19 (Feb 2009) from the International Human Genome Consortium	Annotations	NIH mirror of UCSC Genome Browser	17 May 2013 (Updated weekly Source:UCSC)
Mouse Genome mm8 Build 36, mm8, Mar 2006 from the Mouse Genome Consortium	Annotations	NIH mirror of UCSC Genome Browser	17 May 2013 (Updated weekly Source:UCSC )
Mouse Genome mm9 Build 37, mm9, Jul 2007 from the Mouse Genome Consortium	Annotations	NIH mirror of UCSC Genome Browser	17 May 2013 (Updated weekly Source:UCSC )
Rat Genome May 2006 build, rn4, from the Rat Genome Sequencing Consortium	Annotations	NIH mirror of UCSC genome browser	10 May 2013 (Updated weekly Source:UCSC )
Rhesus genome Jan 2006 assembly from the Baylor Sequencing Center.	Annotations	NIH mirror of UCSC genome browser	25 Jan 2013 (Updated weekly Source:UCSC )
Zebrafish genome Mar 2006 assembly from the Sanger Center.	Annotations	NIH mirror of UCSC genome browser	29 Nov 2011 (Updated weekly Source:UCSC )
Chicken Genome May 2006 assembly from WUSTL.	Prot	NIH mirror of UCSC Genome Browser	05 Apr 2013 (Updated weekly Source:UCSC )
Cow Genome Aug 2006 assembly from the Baylor Sequencing Center	Prot	NIH mirror of UCSC genome browser	31 Jan 2012 (Updated weekly Source:UCSC )
Dog Genome May 2005 assembly from the Broad Institute	Prot	NIH mirror of UCSC genome browser	25 Jan 2013 (Updated weekly Source:UCSC )
Human Genome hg18 Build 36, hg18 (Apr 2006) from the International Human Genome Consortium	Prot	NIH mirror of UCSC Genome Browser	17 May 2013 (Updated weekly Source:UCSC )
Human Genome hg19 Build 37, hg19 (Feb 2009) from the International Human Genome Consortium	Prot	NIH mirror of UCSC Genome Browser	17 May 2013 (Updated weekly Source:UCSC )
Mouse Genome mm8 Build 36, mm8, Mar 2006 from the Mouse Genome Consortium	Prot	NIH mirror of UCSC Genome Browser	17 May 2013 (Updated weekly Source:UCSC )
Mouse Genome mm9 Build 37, mm9, Jul 2007 from the Mouse Genome Consortium	Prot	NIH mirror of UCSC Genome Browser	17 May 2013 (Updated weekly Source:UCSC )
Rat Genome May 2006 build, rn4, from the Rat Genome Sequencing Consortium	Prot	NIH mirror of UCSC genome browser	10 May 2013 (Updated weekly Source:UCSC )
Rhesus genome Jan 2006 assembly from the Baylor Sequencing Center.	Prot	NIH mirror of UCSC genome browser	25 Jan 2013 (Updated weekly Source:UCSC )
Zebrafish genome Mar 2006 assembly from the Sanger Center.	Prot	NIH mirror of UCSC genome browser	29 Nov 2011 (Updated weekly Source:UCSC )
vcf files databases Accessible via
1000 Genomes 20100804 release containing analysis results sets (vcfs) and README files.	Nuc	/fdb/1000genomes/	01 Apr 2013 (Updated occasionally Source:NCBI)
BAM databases Accessible via
1000 Genomes 20100804 release containing analysis results sets (vcfs) and README files.	Alignment	/fdb/1000genomes/ftp/data/	20 May 2013 (Updated occasionally Source:NCBI)

EMBOSS databases

Blast databases

Fasta databases

Mascot databases

PDB databases

CSD databases

PFAM databases

MySQL databases

vcf files databases

BAM databases