Scientific Databases

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Database	Type	Available formats	Location on the Helix Systems	Last updated

1000 Genomes 20100804 release containing analysis results sets (vcfs) and README files.	Nuc	vcf files	/fdb/1000genomes/	01 Apr 2013 (Updated occasionally Source:NCBI.)
	Alignment	BAM	/fdb/1000genomes/ftp/data/	23 Apr 2013 (Updated occasionally Source:NCBI)

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 Source:CCDC)

Chicken Genome May 2006 assembly from WUSTL.	Nuc	MySQL	NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes.	05 Apr 2013 (Updated weekly Source:UCSC .)
	Prot	MySQL	NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes.	05 Apr 2013 (Updated weekly Source:UCSC )
	Annotations	MySQL	NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes.	05 Apr 2013 (Updated weekly Source:UCSC )

Cow Genome Aug 2006 assembly from the Baylor Sequencing Center	Nuc	MySQL	NIH mirror of UCSC genome browser Also available for direct MySQL queries from the Biowulf cluster nodes.	31 Jan 2012 (Updated weekly Source:UCSC .)
	Prot	MySQL	NIH mirror of UCSC genome browser Also available for direct MySQL queries from the Biowulf cluster nodes.	31 Jan 2012 (Updated weekly Source:UCSC )
	Annotations	MySQL	NIH mirror of UCSC genome browser Also available for direct MySQL queries from the Biowulf cluster nodes.	31 Jan 2012 (Updated weekly Source:UCSC )

Dog Genome May 2005 assembly from the Broad Institute	Nuc	MySQL	NIH mirror of UCSC genome browser Also available for direct MySQL queries from the Biowulf cluster nodes.	25 Jan 2013 (Updated weekly Source:UCSC .)
	Prot	MySQL	NIH mirror of UCSC genome browser Also available for direct MySQL queries from the Biowulf cluster nodes.	25 Jan 2013 (Updated weekly Source:UCSC )
	Annotations	MySQL	NIH mirror of UCSC genome browser Also available for direct MySQL queries from the Biowulf cluster nodes.	25 Jan 2013 (Updated weekly Source:UCSC )

Drosophila Drosophila sequences	Nuc	Blast	/fdb/blastdb/drosoph.nt See: Blast (Helix) Blast (Biowulf)	26 Sep 2011 (Updated weekly Source:NCBI .)
	Nuc	Fasta	/fdb/fastadb/drosoph.nt.fas See: Fasta, BLAT.	04 Sep 2012 (Updated weekly Source:NCBI )
	Prot	Blast	/fdb/blastdb/drosoph.aa See: Blast (Helix) Blast (Biowulf)	26 Sep 2011 (Updated weekly Source:NCBI )
	Prot	Fasta	/fdb/fastadb/drosoph.aa.fas See: Fasta, BLAT.	04 Sep 2012 (Updated weekly Source:NCBI )

Drosophila genome April 2006 assembly	Annotations	MySQL	NIH mirror of UCSC genome browser Also available for direct MySQL queries from the Biowulf cluster nodes.	10 May 2013 (Updated weekly Source:UCSC)

EST EST division of Genbank	Nuc	EMBOSS	/fdb/embossdb/est.new See: EMBOSS web interface EMBOSS command-line	18 Apr 2013 (Updated bimonthly after Genbank release Source:NCBI .)

EST - human Human sequences from the EST division of Genbank	Nuc	Blast	/fdb/blastdb/est_human See: Blast (Helix) Blast (Biowulf)	23 May 2012 (Updated weekly Source:NCBI .)
	Nuc	Fasta	/fdb/fastadb/est_human.fas See: Fasta, BLAT.	14 May 2013 (Updated weekly Source:NCBI )

EST - mouse Mouse sequences from the EST division of Genbank.	Nuc	Blast	/fdb/blastdb/est_mouse See: Blast (Helix) Blast (Biowulf)	23 May 2012 (Updated weekly Source:NCBI .)
	Nuc	Fasta	/fdb/fastadb/est_mouse.fas See: Fasta, BLAT.	14 May 2013 (Updated weekly Source:NCBI )

EST - others Non-human, non-mouse sequences from the EST division of Genbank	Nuc	Blast	/fdb/blastdb/est_others See: Blast (Helix) Blast (Biowulf)	23 May 2012 (Updated weekly Source:NCBI .)

Gb_New All sequences added to Genbank since last major release	Nuc	EMBOSS	/fdb/embossdb/gbnew.new See: EMBOSS web interface EMBOSS command-line	18 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	EMBOSS	/fdb/embossdb/genbank.new See: EMBOSS web interface EMBOSS command-line	17 Apr 2013 (Updated bimonthly after Genbank release Source:NCBI .)

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 See: EMBOSS web interface EMBOSS command-line	12 Dec 2012 (Updated bimonthly after Genbank release Source:NCIFCRF)

GP_New All sequences added to GenPept since last major release	Prot	EMBOSS	/fdb/embossdb/gpnew.new See: EMBOSS web interface EMBOSS command-line	02 Oct 2012 (Updated daily Source:NCIFCRF )

HTGs High throughput genome sequences	Nuc	Blast	/fdb/blastdb/htgs See: Blast (Helix) Blast (Biowulf)	21 Apr 2013 (Updated weekly Source:NCBI .)

Human Genome hg18 Build 36, hg18 (Apr 2006) from the International Human Genome Consortium	Nuc	Blast	/fdb/genome/human-apr2006/hs_genome See: Blast (Helix) Blast (Biowulf)	20 May 2011 (Updated after new build release Source:UCSC .)
		Fasta	/fdb/genome/human-apr2006/ See: Fasta, BLAT.	20 May 2011 (Updated after new build release Source:UCSC)
		MySQL	NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes.	17 May 2013 (Updated weekly Source:UCSC )
	Prot	MySQL	NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes.	17 May 2013 (Updated weekly Source:UCSC )
	Annotations	MySQL	NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes.	17 May 2013 (Updated weekly Source:UCSC)

Human Genome hg19 Build 37, hg19 (Feb 2009) from the International Human Genome Consortium	Nuc	Blast	/fdb/blastdb/hs_genome See: Blast (Helix) Blast (Biowulf)	02 May 2013 (Updated after new build release Source:UCSC .)
		Fasta	/fdb/genome/human-feb2009/ See: Fasta, BLAT.	02 May 2013 (Updated after new build release Source:UCSC)
		MySQL	NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes.	17 May 2013 (Updated weekly Source:UCSC )
	Prot	MySQL	NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes.	17 May 2013 (Updated weekly Source:UCSC )
	Annotations	MySQL	NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes.	17 May 2013 (Updated weekly Source:UCSC)

Human Genome Proteins hg18 Build 36, hg18 (Apr 2006) from the International Human Genome Consortium	Prot	Blast	/fdb/genome/human-apr2006/hs_genome.protein See: Blast (Helix) Blast (Biowulf)	28 Apr 2006 (Updated after build release Source:NCBI )
	Prot	Blast	/fdb/genome/human-apr2006/hs_genome.protein See: Blast (Helix) Blast (Biowulf)	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	Fasta	/fdb/fastadb/hs_genome.protein.fas See: Fasta, BLAT.	12 Apr 2010 (Updated after build release Source:NCBI )
	Prot	Blast	/fdb/blastdb/hs_genome.protein See: Blast (Helix) Blast (Biowulf)	05 Nov 2012 (Updated after build release Source:NCBI )

Human Genome RNA hg18 Build 36, hg18 (Apr 2006) from the International Human Genome Consortium	Nuc	Blast	/fdb/genome/human-apr2006/hs_genome.rna See: Blast (Helix) Blast (Biowulf)	28 Apr 2006 (Updated after build release Source:NCBI .)
	Nuc	Fasta	/fdb/genome/human-apr2006/hs_genome.rna.fas See: Fasta, BLAT.	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	Fasta	/fdb/fastadb/hs_genome.rna.fas See: Fasta, BLAT.	12 Apr 2010 (Updated after build release Source:NCBI .)
	Nuc	Blast	/fdb/blastdb/hs_genome.rna See: Blast (Helix) Blast (Biowulf)	05 Nov 2012 (Updated after build release Source:NCBI )

Mito Mitochondrial sequences	Nuc	Blast	/fdb/blastdb/mito.nt See: Blast (Helix) Blast (Biowulf)	13 May 2013 (Updated weekly Source:NCBI .)
	Nuc	Fasta	/fdb/fastadb/mito.nt.fas See: Fasta, BLAT.	14 May 2013 (Updated weekly Source:NCBI )
	Prot	Blast	/fdb/blastdb/mito.aa See: Blast (Helix) Blast (Biowulf)	13 May 2013 (Updated weekly Source:NCBI )
	Prot	Fasta	/fdb/fastadb/mito.aa.fas See: Fasta, BLAT.	14 May 2013 (Updated weekly Source:NCBI )

Mouse Genome mm8 Build 36, mm8, Mar 2006 from the Mouse Genome Consortium	Nuc	Blast	/fdb/genome/mouse-mar2006/mouse_genome See: Blast (Helix) Blast (Biowulf)	09 Nov 2006 (Updated after new build release Source:UCSC .)
		Fasta	/fdb/genome/mouse-mar2006/ See: Fasta, BLAT.	08 Jul 2010 (Updated after new build release Source:UCSC )
		MySQL	NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes.	17 May 2013 (Updated weekly Source:UCSC )
	Prot	MySQL	NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes.	17 May 2013 (Updated weekly Source:UCSC )
	Annotations	MySQL	NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes.	17 May 2013 (Updated weekly Source:UCSC )

Mouse Genome mm9 Build 37, mm9, Jul 2007 from the Mouse Genome Consortium	Nuc	Blast	/fdb/blastdb/mouse_genome See: Blast (Helix) Blast (Biowulf)	25 Mar 2008 (Updated after new build release Source:UCSC .)
		Fasta	/fdb/genome/mouse-jul2007/ See: Fasta, BLAT.	06 Apr 2011 (Updated after new build release Source:UCSC )
		MySQL	NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes.	17 May 2013 (Updated weekly Source:UCSC )
	Prot	MySQL	NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes.	17 May 2013 (Updated weekly Source:UCSC )
	Annotations	MySQL	NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes.	17 May 2013 (Updated weekly Source:UCSC )

Mouse Genome Proteins mm8 Build 36, mm8, Mar 2006 from the Mouse Genome Consortium	Prot	Blast	/fdb/genome/mouse-mar2006/mouse_genome.protein See: Blast (Helix) Blast (Biowulf)	09 Nov 2006 (Updated weekly Source:NCBI )
	Prot	Fasta	/fdb/genome/mouse-mar2006/mouse_genome.protein.fas See: Fasta, BLAT.	09 Nov 2006 (Updated weekly Source:NCBI )

Mouse Genome Proteins mm9 Build 37, mm9, Jul 2007 from the Mouse Genome Consortium	Prot	Blast	/fdb/genome/mouse-mar2006/mouse_genome.protein See: Blast (Helix) Blast (Biowulf)	09 Nov 2006 (Updated weekly Source:NCBI )
	Prot	Fasta	/fdb/fastadb/mouse_genome.protein.fas See: Fasta, BLAT.	25 Mar 2008 (Updated weekly Source:NCBI )

Mouse Genome RNA mm8 Build 36, mm8, Mar 2006 from the Mouse Genome Consortium	Nuc	Blast	/fdb/genome/mouse-mar2006/mouse_genome.rna See: Blast (Helix) Blast (Biowulf)	09 Nov 2006 (Updated after release Source:NCBI .)

Mouse Genome RNA mm9 Build 37, mm9, Jul 2007 from the Mouse Genome Consortium	Nuc	Blast	/fdb/blastdb/mouse_genome.rna See: Blast (Helix) Blast (Biowulf)	22 Oct 2012 (Updated after release Source:NCBI .)
	Nuc	Fasta	/fdb/fastadb/mouse_genome.rna.fas See: Fasta, BLAT.	25 Mar 2008 (Updated after release Source:NCBI )

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 Source:NCBI )

NCBI nr NCBI's nonredundant Genbank CDS translations + PDB + SwissProt	Prot	Blast	/fdb/blastdb/nr See: Blast (Helix) Blast (Biowulf)	25 Apr 2013 (Updated weekly Source:NCBI )
		Fasta	/fdb/fastadb/nr.aa.fas See: Fasta, BLAT.	14 May 2013 (Updated weekly Source:NCBI )
		Mascot	biospec.nih.gov Mascot search engine	12 May 2013 (Updated weekly Source:NCBI )

NCBI nt All GenBank+EMBL+DDBJ (but no EST, STS, GSS, HTG). No longer nonredundant.	Nuc	Blast	/fdb/blastdb/nt See: Blast (Helix) Blast (Biowulf)	07 May 2013 (Updated weekly Source:NCBI .)
	Nuc	Fasta	/fdb/fastadb/nt.fas See: Fasta, BLAT.	14 May 2013 (Updated weekly Source:NCBI )

NIH-Specific A collection of NIH-specific databases requested by NIH Mascot users.	Prot	Mascot	biospec.nih.gov Mascot search engine	15 May 2013 (Updated as requested Source:NIH)

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 Source:PFAM )

Prints Protein fingerprints, groups of conserved motifs used to characterize a protein family.	Patterns	EMBOSS	used internally by Emboss See: EMBOSS web interface EMBOSS command-line	22 Apr 2013 (Updated after new Prints release Source:EBI)

Prosite A database/dictionary of protein sites and patterns. More information at Expasy.	Patterns	EMBOSS	used internally by Emboss See: EMBOSS web interface EMBOSS command-line	15 May 2013 (Updated every 2 months Source:Expasy )

Protein Data Bank An archive of experimentally determined three-dimensional strtures of biological macromolecules. More information at the PDB.	Nuc	Blast	/fdb/blastdb/pdbnt See: Blast (Helix) Blast (Biowulf)	08 May 2013 (Updated weekly Source:NCBI .)
	Nuc	Fasta	/fdb/fastadb/pdb.nt.fas See: Fasta, BLAT.	14 May 2013 (Updated weekly Source:NCBI )
	Prot	Blast	/fdb/blastdb/pdbaa See: Blast (Helix) Blast (Biowulf)	08 May 2013 (Updated weekly Source:NCBI )
	Prot	Fasta	/fdb/fastadb/pdb.aa.fas See: Fasta, BLAT.	14 May 2013 (Updated weekly Source:NCBI )
	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.	19 May 2013 (Updated daily Source:PDB )

Rat Genome May 2006 build, rn4, from the Rat Genome Sequencing Consortium	Nuc	MySQL	NIH mirror of UCSC genome browser Also available for direct MySQL queries from the Biowulf cluster nodes.	10 May 2013 (Updated weekly Source:UCSC .)
	Prot	MySQL	NIH mirror of UCSC genome browser Also available for direct MySQL queries from the Biowulf cluster nodes.	10 May 2013 (Updated weekly Source:UCSC )
	Annotations	MySQL	NIH mirror of UCSC genome browser Also available for direct MySQL queries from the Biowulf cluster nodes.	10 May 2013 (Updated weekly Source:UCSC )

REBASE About restriction enzymes, recognition sequences, cleavage sites... More information at REBASE.	Enzymes	EMBOSS	used internally by Emboss See: EMBOSS web interface EMBOSS command-line	15 May 2013 (Updated every month Source:REBASE )

Refseq Human Genomic Refseq Human (NC_######) chromosome records with gap adjusted concatenated NT_ contigs	Nuc	Blast	/fdb/blastdb/human_genomic See: Blast (Helix) Blast (Biowulf)	10 May 2013 (Updated weekly Source:NCBI.)
	Nuc	Fasta	/fdb/fastadb/ref.human.genomic.fas See: Fasta, BLAT.	14 May 2013 (Updated weekly Source:NCBI)

Refseq Human Proteins A comprehensive, integrated, non-redundant set of sequences. More info at NCBI	Prot	Blast	/fdb/blastdb/human.protein See: Blast (Helix) Blast (Biowulf)	13 May 2013 (Updated weekly Source:NCBI)
	Prot	Fasta	/fdb/fastadb/ref.human.protein.fas See: Fasta, BLAT.	14 May 2013 (Updated weekly Source:NCBI)

Refseq Human RNA A comprehensive, integrated, non-redundant set of sequences. More info at NCBI	Nuc	Blast	/fdb/blastdb/human.rna See: Blast (Helix) Blast (Biowulf)	13 May 2013 (Updated weekly Source:NCBI.)
	Nuc	Fasta	/fdb/fastadb/ref.human.rna.fas See: Fasta, BLAT.	14 May 2013 (Updated weekly Source:NCBI)

Refseq Mouse Proteins A comprehensive, integrated, non-redundant set of sequences. More info at NCBI	Prot	Blast	/fdb/blastdb/mouse.protein See: Blast (Helix) Blast (Biowulf)	13 May 2013 (Updated weekly Source:NCBI)
	Prot	Fasta	/fdb/fastadb/ref.mouse.protein.fas See: Fasta, BLAT.	14 May 2013 (Updated weekly Source:NCBI)

Refseq Mouse RNA A comprehensive, integrated, non-redundant set of sequences. More info at NCBI	Nuc	Blast	/fdb/blastdb/mouse.rna See: Blast (Helix) Blast (Biowulf)	13 May 2013 (Updated weekly Source:NCBI.)
	Nuc	Fasta	/fdb/fastadb/ref.mouse.rna.fas See: Fasta, BLAT.	14 May 2013 (Updated weekly Source:NCBI)

Refseq Other Genomic RefSeq chromosome records (NC_######) for organisms other than human	Nuc	Blast	/fdb/blastdb/other_genomic See: Blast (Helix) Blast (Biowulf)	28 Feb 2013 (Updated weekly Source:NCBI .)
	Nuc	Fasta	/fdb/fastadb/ref.other.genomic.fas See: Fasta, BLAT.	14 May 2013 (Updated weekly Source:NCBI)

Refseqaa NCBI's comprehensive, integrated, non-redundant set of protein sequences for major research organisms.	Prot	EMBOSS	/fdb/embossdb/refseqaa.new See: EMBOSS web interface EMBOSS command-line	08 May 2013 (Updated weekly Source:NCBI)

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 See: EMBOSS web interface EMBOSS command-line	08 May 2013 (Updated weekly Source:NCBI.)

Rhesus genome Jan 2006 assembly from the Baylor Sequencing Center.	Nuc	MySQL	NIH mirror of UCSC genome browser Also available for direct MySQL queries from the Biowulf cluster nodes.	25 Jan 2013 (Updated weekly Source:UCSC .)
	Prot	MySQL	NIH mirror of UCSC genome browser Also available for direct MySQL queries from the Biowulf cluster nodes.	25 Jan 2013 (Updated weekly Source:UCSC )
	Annotations	MySQL	NIH mirror of UCSC genome browser Also available for direct MySQL queries from the Biowulf cluster nodes.	25 Jan 2013 (Updated weekly Source:UCSC )

Sp_Trembl SwissProt + Trembl (a computer-annotated supplement of SwissProt)	Prot	Mascot	biospec.nih.gov Mascot search engine	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	Blast	/fdb/blastdb/swissprot See: Blast (Helix) Blast (Biowulf)	13 May 2013 (Updated weekly Source:NCBI)
		Fasta	/fdb/fastadb/swissprot.aa.fas See: Fasta, BLAT.	14 May 2013 (Updated weekly Source:NCBI )
		Mascot	biospec.nih.gov Mascot search engine	05 May 2013 (Updated weekly Source:Expasy )

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 See: EMBOSS web interface EMBOSS command-line	01 May 2013 (Updated weekly Source:Uniprot)

Yeast Yeast sequences	Nuc	Blast	/fdb/blastdb/yeast.nt See: Blast (Helix) Blast (Biowulf)	26 Sep 2011 (Updated weekly Source:NCBI .)
	Nuc	Fasta	/fdb/fastadb/yeast.nt.fas See: Fasta, BLAT.	04 Sep 2012 (Updated weekly Source:NCBI )
	Prot	Blast	/fdb/blastdb/yeast.aa See: Blast (Helix) Blast (Biowulf)	26 Sep 2011 (Updated weekly Source:NCBI )
	Prot	Fasta	/fdb/fastadb/yeast.aa.fas See: Fasta, BLAT.	30 Jun 2011 (Updated weekly Source:NCBI )

Zebrafish genome Mar 2006 assembly from the Sanger Center.	Nuc	MySQL	NIH mirror of UCSC genome browser Also available for direct MySQL queries from the Biowulf cluster nodes.	29 Nov 2011 (Updated weekly Source:UCSC .)
	Prot	MySQL	NIH mirror of UCSC genome browser Also available for direct MySQL queries from the Biowulf cluster nodes.	29 Nov 2011 (Updated weekly Source:UCSC )
	Annotations	MySQL	NIH mirror of UCSC genome browser Also available for direct MySQL queries from the Biowulf cluster nodes.	29 Nov 2011 (Updated weekly Source:UCSC )