Scientific Databases

Sorted by database type /database /format

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Database	Type	Available formats	Location on the Helix Systems	Accessible via	Last updated
Nuc databases
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.	30 Dec 2007 (Updated weekly Source:UCSC )
Cow Genome Mar 2005 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.	24 Mar 2008 (Updated weekly Source:UCSC )
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.	30 Dec 2007 (Updated weekly Source:UCSC )
Drosophila Drosophila sequences	Nuc	Blast	/fdb/blastdb/drosoph.nt	Blast (Helix) Blast (Biowulf)	25 Jul 2005 (Updated weekly Source:NCBI )
		Fasta	/fdb/fastadb/drosoph.nt.fas	Fasta, BLAT. User programs.	25 Jul 2005 (Updated weekly Source:NCBI )
		WU-Blast	/fdb/wublastdb/drosoph.nt	WU-Blast	25 Aug 2009 (Updated weekly Source:NCBI )
E.Coli E.Coli sequences	Nuc	Blast	/fdb/blastdb/ecoli.nt	Blast (Helix) Blast (Biowulf)	25 Jul 2005 (Updated weekly Source:NCBI )
		Fasta	/fdb/fastadb/ecoli.nt.fas	Fasta, BLAT. User programs.	25 Jul 2005 (Updated weekly Source:NCBI )
		WU-Blast	/fdb/wublastdb/ecoli.nt	WU-Blast	25 Aug 2009 (Updated weekly Source:NCBI )
		Blast	/fdb/blastdb/ecoli.nt	Blast (Helix) Blast (Biowulf)	25 Jul 2005 (Updated weekly Source:NCBI )
EST EST division of Genbank	Nuc	EMBOSS	/fdb/embossdb/est.new	EMBOSS web interface & EMBOSS command-line	30 Oct 2009 (Updated bimonthly after Genbank release Source:NCBI )
EST - human Human sequences from the EST division of Genbank	Nuc	Blast	/fdb/blastdb/est_human	Blast (Helix) Blast (Biowulf)	19 Nov 2009 (Updated weekly Source:NCBI )
		WU-Blast	/fdb/wublastdb/est_human	WU-Blast	24 Nov 2009 (Updated weekly Source:NCBI )
		Fasta	/fdb/fastadb/est_human.fas	Fasta, BLAT. User programs.	24 Nov 2009 (Updated weekly Source:NCBI )
EST - mouse Mouse sequences from the EST division of Genbank.	Nuc	Blast	/fdb/blastdb/est_mouse	Blast (Helix) Blast (Biowulf)	19 Nov 2009 (Updated weekly Source:NCBI )
		WU-Blast	/fdb/wublastdb/est_mouse	WU-Blast	24 Nov 2009 (Updated weekly Source:NCBI )
		Fasta	/fdb/fastadb/est_mouse.fas	Fasta, BLAT. User programs.	24 Nov 2009 (Updated weekly Source:NCBI )
EST - others Non-human, non-mouse sequences from the EST division of Genbank	Nuc	Blast	/fdb/blastdb/est_others	Blast (Helix) Blast (Biowulf)	19 Nov 2009 (Updated weekly Source:NCBI )
Gb_New All sequences added to Genbank since last major release	Nuc	EMBOSS	/fdb/embossdb/gbnew.new	EMBOSS web interface & EMBOSS command-line	24 Nov 2009 (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	EMBOSS web interface & EMBOSS command-line	21 Oct 2009 (Updated bimonthly after Genbank release Source:NCBI )
HTGs High throughput genome sequences	Nuc	Blast	/fdb/blastdb/htgs	Blast (Helix) Blast (Biowulf)	17 Nov 2009 (Updated weekly Source:NCBI )
Human Genome Build 36, hg18 (April 2006) from the International Human Genome Consortium	Nuc	Blast	/fdb/blastdb/hs_genome	Blast (Helix) Blast (Biowulf)	01 May 2006 (Updated after new build release Source:UCSC )
		Fasta	/fdb/genome/human-apr2006/	Fasta, BLAT. User programs.	01 May 2006 (Updated after new build release Source:UCSC)
		MySQL	NIH mirror of UCSC genome browser	NIH mirror of UCSC Genome Browser Also available for direct MySQL queries from the Biowulf cluster nodes.	23 Jul 2009 (Updated weekly Source:UCSC )
		WU-Blast	/fdb/wublastdb/hs_genome	WU-Blast	01 May 2006 (Updated weekly Source:UCSC)
Human Genome RNA Build 36, hg18 (April 2006) from the International Human Genome Consortium	Nuc	Fasta	/fdb/fastadb/hs_genome.rna.fas	Fasta, BLAT. User programs.	28 Apr 2006 (Updated after build release Source:NCBI )
		Blast	/fdb/blastdb/hs_genome.rna	Blast (Helix) Blast (Biowulf)	11 Aug 2009 (Updated after build release Source:NCBI )
		WU-Blast	/fdb/wublastdb/hs_genome.rna	WU-Blast	01 May 2006 (Updated after build release Source:NCBI )
Mito Mitochondrial sequences	Nuc	Blast	/fdb/blastdb/mito.nt	Blast (Helix) Blast (Biowulf)	25 Jul 2005 (Updated weekly Source:NCBI )
		Fasta	/fdb/fastadb/mito.nt.fas	Fasta, BLAT. User programs.	25 Jul 2005 (Updated weekly Source:NCBI )
		WU-Blast	/fdb/wublastdb/mito.nt	WU-Blast	25 Aug 2009 (Updated weekly Source:NCBI )
Mouse Genome 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 Source:UCSC )
		WU-Blast	/fdb/wublastdb/mouse_genome	WU-Blast	25 Mar 2008 (Updated after new build release Source:UCSC )
		Fasta	/fdb/genome/mouse-mar2006/	Fasta, BLAT. User programs.	26 Mar 2008 (Updated after new build release Source:UCSC )
		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 Oct 2009 (Updated weekly Source:UCSC )
Mouse Genome RNA Build 37, mm9, Jul 2007 from the Mouse Genome Consortium	Nuc	Blast	/fdb/blastdb/mouse_genome.rna	Blast (Helix) Blast (Biowulf)	26 Mar 2008 (Updated after release Source:NCBI )
		Fasta	/fdb/fastadb/mouse_genome.rna.fas	Fasta, BLAT. User programs.	25 Mar 2008 (Updated after release Source:NCBI )
		WU-Blast	/fdb/wublastdb/mouse.rna	WU-Blast	25 Mar 2008 (Updated after release Source:NCBI )
NCBI nt All GenBank+EMBL+DDBJ (but no EST, STS, GSS, HTG). No longer nonredundant.	Nuc	Blast	/fdb/blastdb/nt	Blast (Helix) Blast (Biowulf)	18 Nov 2009 (Updated weekly Source:NCBI )
		WU-Blast	/fdb/wublastdb/nt	WU-Blast	24 Nov 2009 (Updated weekly Source:NCBI )
		Fasta	/fdb/fastadb/nt.fas	Fasta, BLAT. User programs.	24 Nov 2009 (Updated weekly Source:NCBI )
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)	19 Nov 2009 (Updated weekly Source:NCBI )
		Fasta	/fdb/fastadb/pdb.nt.fas	Fasta, BLAT. User programs.	24 Nov 2009 (Updated weekly Source:NCBI )
		WU-Blast	/fdb/wublastdb/pdb.nt	WU-Blast	24 Nov 2009 (Updated weeekly Source:NCBI )
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.	29 Dec 2007 (Updated weekly Source:UCSC )
Refseq Human Genomic Refseq Human (NC_######) chromosome records with gap adjusted concatenated NT_ contigs	Nuc	Blast	/fdb/blastdb/human_genomic	Blast (Helix) Blast (Biowulf)	19 Nov 2009 (Updated weekly Source:NCBI)
	Nuc	Fasta	/fdb/fastadb/ref.human.genomic.fas	Fasta, BLAT. User programs.	24 Nov 2009 (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	Blast (Helix) Blast (Biowulf)	23 Nov 2009 (Updated weekly Source:NCBI)
		Fasta	/fdb/fastadb/ref.human.rna.fas	Fasta, BLAT. User programs.	24 Nov 2009 (Updated weekly Source:NCBI)
		WU-Blast	/fdb/wublastdb/ref.human.rna	WU-Blast	24 Nov 2009 (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	Blast (Helix) Blast (Biowulf)	23 Nov 2009 (Updated weekly Source:NCBI)
		Fasta	/fdb/fastadb/ref.mouse.rna.fas	Fasta, BLAT. User programs.	24 Nov 2009 (Updated weekly Source:NCBI)
		WU-Blast	/fdb/wublastdb/ref.mouse.rna	WU-Blast	24 Nov 2009 (Updated weekly Source:NCBI)
Refseq Other Genomic RefSeq chromosome records (NC_######) for organisms other than human	Nuc	Blast	/fdb/blastdb/other_genomic	Blast (Helix) Blast (Biowulf)	17 Nov 2009 (Updated weekly Source:NCBI )
	Nuc	Fasta	/fdb/fastadb/ref.other.genomic.fas	Fasta, BLAT. User programs.	24 Nov 2009 (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	EMBOSS web interface & EMBOSS command-line	18 Nov 2009 (Updated weekly Source:NCBI)
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.	29 Dec 2007 (Updated weekly Source:UCSC )
UniVec Core A non-redundant database of sequences commonly attached to cDNA or genomic DNA during the cloning process. Includes only oligonucleotides and vectors consisting of bacterial, phage, viral, yeast or synthetic sequences, but not vectors that include sequences of mammalian origin.	Nuc	Blast	/fdb/blastdb/univec_core	Blast (Helix) Blast (Biowulf)	28 Apr 2008 (Updated once Source:NCBI)
Yeast Yeast sequences	Nuc	Blast	/fdb/blastdb/yeast.nt	Blast (Helix) Blast (Biowulf)	25 Jul 2005 (Updated weekly Source:NCBI )
		Fasta	/fdb/fastadb/yeast.nt.fas	Fasta, BLAT. User programs.	25 Jul 2005 (Updated weekly Source:NCBI )
		WU-Blast	/fdb/wublastdb/yeast.nt	WU-Blast	25 Aug 2009 (Updated weekly Source:NCBI )
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.	30 Dec 2007 (Updated weekly Source:UCSC )
3-D databases
Cambridge Structural Database Crystal structure information for over 165,000 organic and organometallic compounds. More info at CCDC.	3-D	CSD	/local/csd	Quest	03 Apr 2009 (Updated every 3 months Source:CCDC)
Protein Data Bank An archive of experimentally determined three-dimensional strtures of biological macromolecules. More information at the PDB.	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.	25 Nov 2009 (Updated daily Source:PDB )
Families databases
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 )
Patterns databases
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	18 Nov 2009 (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	EMBOSS web interface & EMBOSS command-line	18 Nov 2009 (Updated every 2 months Source:Expasy )
Enzymes databases
REBASE About restriction enzymes, recognition sequences, cleavage sites... More information at REBASE.	Enzymes	EMBOSS	used internally by Emboss	EMBOSS web interface & EMBOSS command-line	18 Nov 2009 (Updated every month Source:REBASE )
Info databases
Transfac Transcription factor database, most recent version from www.biobase.de.	Info	EMBOSS	used internally by Emboss	EMBOSS web interface & EMBOSS command-line	04 Sep 2009 (Updated with new Transfac release. Source:Biobase )
Annotations databases
Chicken Genome May 2006 assembly from WUSTL.	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.	30 Dec 2007 (Updated weekly Source:UCSC )
Cow Genome Mar 2005 assembly from the Baylor Sequencing Center	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.	24 Mar 2008 (Updated weekly Source:UCSC )
Dog Genome May 2005 assembly from the Broad Institute	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.	30 Dec 2007 (Updated weekly Source:UCSC )
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.	17 Jul 2009 (Updated weekly Source:UCSC)
Human Genome Build 36, hg18 (April 2006) from the International Human Genome Consortium	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.	23 Jul 2009 (Updated weekly Source:UCSC)
Mouse Genome Build 37, mm9, Jul 2007 from the Mouse Genome Consortium	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 Oct 2009 (Updated weekly Source:UCSC )
Rat Genome May 2006 build, rn4, from the Rat Genome Sequencing Consortium	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 Dec 2007 (Updated weekly Source:UCSC )
Rhesus genome Jan 2006 assembly from the Baylor Sequencing Center.	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 Dec 2007 (Updated weekly Source:UCSC )
Zebrafish genome Mar 2006 assembly from the Sanger Center.	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.	30 Dec 2007 (Updated weekly Source:UCSC )
Prot databases
Chicken Genome May 2006 assembly from WUSTL.	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.	30 Dec 2007 (Updated weekly Source:UCSC )
Cow Genome Aug 2006 assembly from the Baylor Sequencing Center	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.	24 Mar 2008 (Updated weekly Source:UCSC )
Dog Genome May 2005 assembly from the Broad Institute	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.	30 Dec 2007 (Updated weekly Source:UCSC )
Drosophila Drosophila sequences	Prot	Blast	/fdb/blastdb/drosoph.aa	Blast (Helix) Blast (Biowulf)	25 Jul 2005 (Updated weekly Source:NCBI )
		Fasta	/fdb/fastadb/drosoph.aa.fas	Fasta, BLAT. User programs.	25 Jul 2005 (Updated weekly Source:NCBI )
		WU-Blast	/fdb/wublastdb/drosoph.aa	WU-Blast	25 Aug 2009 (Updated weekly Source:NCBI )
E.Coli E.Coli sequences	Prot	Blast	/fdb/blastdb/ecoli.aa	Blast (Helix) Blast (Biowulf)	19 Mar 2006 (Updated weekly Source:NCBI )
		Fasta	/fdb/fastadb/ecoli.aa.fas	Fasta, BLAT. User programs.	25 Jul 2005 (Updated weekly Source:NCBI )
		WU-Blast	/fdb/wublastdb/ecoli.aa	WU-Blast	25 Aug 2009 (Updated weekly 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	EMBOSS web interface & EMBOSS command-line	28 Oct 2009 (Updated bimonthly after Genbank release Source:NCIFCRF)
GP_New All sequences added to GenPept since last major release	Prot	EMBOSS	/fdb/embossdb/gpnew.new	EMBOSS web interface & EMBOSS command-line	24 Nov 2009 (Updated daily Source:NCIFCRF )
Human Genome Build 36, hg18 (April 2006) from the International Human Genome Consortium	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.	23 Jul 2009 (Updated weekly Source:UCSC )
Human Genome Proteins Build 36, hg18 (April 2006) from the International Human Genome Consortium	Prot	Fasta	/fdb/fastadb/hs_genome.protein.fas	Fasta, BLAT. User programs.	28 Apr 2006 (Updated after build release Source:NCBI )
		WU-Blast	/fdb/wublastdb/hs_genome.protein	WU-Blast	01 May 2006 (Updated after build release Source:NCBI )
		Blast	/fdb/blastdb/hs_genome.protein	Blast (Helix) Blast (Biowulf)	11 Aug 2009 (Updated after build release Source:NCBI )
Mito Mitochondrial sequences	Prot	Blast	/fdb/blastdb/mito.aa	Blast (Helix) Blast (Biowulf)	25 Jul 2005 (Updated weekly Source:NCBI )
		Fasta	/fdb/fastadb/mito.aa.fas	Fasta, BLAT. User programs.	25 Jul 2005 (Updated weekly Source:NCBI )
		WU-Blast	/fdb/wublastdb/mito.aa	WU-Blast	29 Oct 2008 (Updated weekly Source:NCBI )
Mouse Genome Build 37, mm9, Jul 2007 from the Mouse Genome Consortium	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 Oct 2009 (Updated weekly Source:UCSC )
Mouse Genome Proteins Build 37, mm9, Jul 2007 from the Mouse Genome Consortium	Prot	Blast	/fdb/blastdb/mouse_genome.protein	Blast (Helix) Blast (Biowulf)	26 Mar 2008 (Updated weekly Source:NCBI )
		Fasta	/fdb/fastadb/mouse_genome.protein.fas	Fasta, BLAT. User programs.	25 Mar 2008 (Updated weekly Source:NCBI )
		WU-Blast	/fdb/wublastdb/mouse_genome.protein	WU-Blast	25 Mar 2008 (Updated weekly Source:NCBI )
MSDB A nonredundant protein sequence database designed specifically for mass-spec applications.	Prot	Mascot	biospec.nih.gov	Mascot search engine	20 Jun 2008 (Updated weekly Source:NCBI )
NCBI nr NCBI's nonredundant Genbank CDS translations + PDB + SwissProt	Prot	Blast	/fdb/blastdb/nr	Blast (Helix) Blast (Biowulf)	19 Nov 2009 (Updated weekly Source:NCBI )
		Fasta	/fdb/fastadb/nr.aa.fas	Fasta, BLAT. User programs.	24 Nov 2009 (Updated weekly Source:NCBI )
		Mascot	biospec.nih.gov	Mascot search engine	24 Nov 2009 (Updated weekly Source:NCBI )
		WU-Blast	/fdb/wublastdb/nr	WU-Blast	24 Nov 2009 (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	13 Nov 2009 (Updated as requested Source:NIH)
Protein Data Bank An archive of experimentally determined three-dimensional strtures of biological macromolecules. More information at the PDB.	Prot	Blast	/fdb/blastdb/pdbaa	Blast (Helix) Blast (Biowulf)	19 Nov 2009 (Updated weekly Source:NCBI )
		Fasta	/fdb/fastadb/pdb.aa.fas	Fasta, BLAT. User programs.	24 Nov 2009 (Updated weekly Source:NCBI )
		WU-Blast	/fdb/wublastdb/pdb.aa	WU-Blast	24 Nov 2009 (Updated weekly Source:NCBI )
Rat Genome May 2006 build, rn4, from the Rat Genome Sequencing Consortium	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 Dec 2007 (Updated weekly Source:UCSC )
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)	23 Nov 2009 (Updated weekly Source:NCBI)
		Fasta	/fdb/fastadb/ref.human.protein.fas	Fasta, BLAT. User programs.	24 Nov 2009 (Updated weekly Source:NCBI)
		WU-Blast	/fdb/wublastdb/ref.human.protein	WU-Blast	24 Nov 2009 (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	Blast (Helix) Blast (Biowulf)	23 Nov 2009 (Updated weekly Source:NCBI)
		Fasta	/fdb/fastadb/ref.mouse.protein.fas	Fasta, BLAT. User programs.	24 Nov 2009 (Updated weekly Source:NCBI)
		WU-Blast	/fdb/wublastdb/ref.mouse.protein	WU-Blast	24 Nov 2009 (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	EMBOSS web interface & EMBOSS command-line	18 Nov 2009 (Updated weekly Source:NCBI)
Rhesus genome Jan 2006 assembly from the Baylor Sequencing Center.	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 Dec 2007 (Updated weekly Source:UCSC )
Sp_Trembl SwissProt + Trembl (a computer-annotated supplement of SwissProt)	Prot	Mascot	biospec.nih.gov	Mascot search engine	08 Nov 2009 (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	Blast (Helix) Blast (Biowulf)	19 Nov 2009 (Updated weekly Source:NCBI)
		Fasta	/fdb/fastadb/swissprot.aa.fas	Fasta, BLAT. User programs.	24 Nov 2009 (Updated weekly Source:NCBI )
		Mascot	biospec.nih.gov	Mascot search engine	08 Nov 2009 (Updated weekly Source:Expasy )
		WU-Blast	/fdb/wublastdb/swissprot.aa	WU-Blast	24 Nov 2009 (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	EMBOSS	/fdb/embossdb/uniprot	EMBOSS web interface & EMBOSS command-line	04 Nov 2009 (Updated weekly Source:Uniprot)
Yeast Yeast sequences	Prot	Blast	/fdb/blastdb/yeast.aa	Blast (Helix) Blast (Biowulf)	25 Jul 2005 (Updated weekly Source:NCBI )
		Fasta	/fdb/fastadb/yeast.aa.fas	Fasta, BLAT. User programs.	25 Jul 2005 (Updated weekly Source:NCBI )
		WU-Blast	/fdb/wublastdb/yeast.aa	WU-Blast	25 Aug 2009 (Updated weekly Source:NCBI )
Zebrafish genome Mar 2006 assembly from the Sanger Center.	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.	30 Dec 2007 (Updated weekly Source:UCSC )

Nuc databases

3-D databases

Families databases

Patterns databases

Enzymes databases

Info databases

Annotations databases

Prot databases