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最新生物信息学常用数据库(更新到2012.4.3)  

2012-04-12 08:46:02|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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DNA databanks

Name Version Date of preparation Description
Embl 111 3 Apr 2012 06:35 EMBL Nucleotide Sequence Database
Genbank 187.0 17 Mar 2012 08:57 NIH DNA sequence database
Imgt 201147-6 17 Mar 2012 15:11 IMGT/LIGM-DB, ImMunoGeneTics sequence database
Nt - 5 Apr 2012 11:57 Nucleotide sequence database, minimally non-redundant
RefSeq 52 20 Mar 2012 17:48 NCBI Reference Sequence (RefSeq) Database
Vector - 20 Mar 2012 13:40 Vector subset of GenBank(R), NCBI
WGS - 21 Mar 2012 10:00 Genbank - Whole Genome Shotgun

Protein databanks

Name Version Date of preparation Description
Genpept 187.0 4 Apr 2012 23:07 Translations of Genbank
Nrprot 04.6 4 Apr 2012 13:20 NCBI non-redundant: (Genbank CDS translations+PDB+Swissprot+PIR)
UniRef90 - 20 Mar 2012 14:19 Clustered sets of sequences from UniProt Knowledgebase
Uniprot 2012_03 4 Apr 2012 09:09 Universal Protein Resource = SwissProt + TrEMBL + PIR

Structure databanks

Name Version Date of preparation Description
Dssp - 23 Mar 2012 14:56 Secondary structure assignments database
Hssp - 6 Apr 2012 17:52 Homology-derived secondary structure of proteins database
Pdb - 5 Apr 2012 15:48 RCSB Protein Databank

Genome databanks

Name Version Date of preparation Description
Borrelia - 16 Mar 2012 14:27 Borrelia burgdorferi B31, complete genome
Bsubtilis - 16 Mar 2012 14:32 Bacillus subtilis subsp. subtilis str. 168, complete genome
Cpneumoniae - 16 Mar 2012 14:33 Chlamydophila pneumoniae CWL029, complete genome
Ecoli - 16 Mar 2012 14:34 Escherichia coli K12, complete genome
Genitalium - 17 Mar 2012 09:08 Mycoplasma genitalium G-37, complete genome
Hpylori - 17 Mar 2012 13:22 Helicobacter pylori 26695, complete genome
Mtuberculosis - 17 Mar 2012 15:12 Mycobacterium tuberculosis H37Rv, complete genome
Pneumoniae - 17 Mar 2012 16:25 Mycoplasma pneumoniae M129, complete genome
UFMG - 20 Mar 2012 09:56 UnFinished Microbial Genomes (UFMG)
Yeast - 20 Mar 2012 15:15 Yeast chromosomes
Ypestis - 20 Mar 2012 15:15 Yersinia pestis unfinished genome

Other databanks

Name Version Date of preparation Description
Alu - 15 Mar 2012 20:33 Select Alu repeats from REPBASE
Enzyme 2012046 26 Jan 2012 01:49 Enzyme Nomenclature Database
Epd 105 30 Mar 2011 22:03 Eukaryotic Promoter Database
Jaspar - 24 Jul 2009 15:39 High-quality transcription factor binding profile database
Pfam 26.0 5 Apr 2012 16:50 Collection of Protein Domain Families
Prints 41.1 30 Mar 2011 15:53 Protein Motif Fingerprint Database
Prosite 20.79 26 Jan 2012 01:51 Dictionary of Protein Sites and Patterns
RDPII 10_28 5 Apr 2012 13:42 Ribosomal Database Project II database
Rebase 204 5 Apr 2012 13:50 The Restriction Enzyme Database
Taxodb - 31 Jan 2012 04:51 Taxonomy database

Detailed list


Alu
Version -
Date of preparation 15 Mar 2012 20:33
Description Select Alu repeats from REPBASE
Origin (ftp) ftp.ncbi.nih.gov
Updates frequency variable
Other informations http://www.ncbi.nlm.nih.gov/mapview/
Sections alunuc Nucleic sequences
alupro Protein sequences

Borrelia
Version -
Date of preparation 16 Mar 2012 14:27
Description Borrelia burgdorferi B31, complete genome
Origin (ftp) ftp.ncbi.nih.gov
Updates frequency variable
Other informations http://www.ncbi.nlm.nih.gov/genome/738?project_id=3
Sections borrelia full bank

Bsubtilis
Version -
Date of preparation 16 Mar 2012 14:32
Description Bacillus subtilis subsp. subtilis str. 168, complete genome
Origin (ftp) ftp.ncbi.nih.gov
Updates frequency variable
Other informations http://www.ncbi.nlm.nih.gov/genome/665?project_id=76
Sections bsubtilis full bank

Cpneumoniae
Version -
Date of preparation 16 Mar 2012 14:33
Description Chlamydophila pneumoniae CWL029, complete genome
Origin (ftp) ftp.ncbi.nih.gov
Updates frequency variable
Other informations http://www.ncbi.nlm.nih.gov/genome/171?project_id=248
Sections cpneumoniae full bank

Dssp
Version -
Date of preparation 23 Mar 2012 14:56
Description Secondary structure assignments database
Origin (ftp) rsync.cmbi.ru.nl
Updates frequency variable
Other informations http://swift.cmbi.ru.nl/gv/dssp/

Ecoli
Version -
Date of preparation 16 Mar 2012 14:34
Description Escherichia coli K12, complete genome
Origin (ftp) ftp.ncbi.nih.gov
Updates frequency variable
Other informations http://www.ncbi.nlm.nih.gov/genome/167?project_id=225
Sections ecoli full bank

Embl
Version 111
Date of preparation 3 Apr 2012 06:35
Description EMBL Nucleotide Sequence Database
Origin (ftp) ftp.ebi.ac.uk
Updates frequency daily
Other informations http://www.ebi.ac.uk/embl/Documentation/
Sections embl_new updates
embl release + updates

Enzyme
Version 2012046
Date of preparation 26 Jan 2012 01:49
Description Enzyme Nomenclature Database
Origin (ftp) ftp.expasy.ch
Updates frequency variable
Other informations http://www.expasy.ch/enzyme/
Sections enzyme full bank

Epd
Version 105
Date of preparation 30 Mar 2011 22:03
Description Eukaryotic Promoter Database
Origin (ftp) ftp.epd.unil.ch
Updates frequency variable
Other informations http://epd.vital-it.ch/
Sections epd full bank

Genbank
Version 187.0
Date of preparation 17 Mar 2012 08:57
Description NIH DNA sequence database
Origin (ftp) ftp.ncbi.nih.gov
Updates frequency daily
Other informations http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html
Sections genbank_new updates
genbank release + updates
gbbct Bacterial
gbcon Constructed Sequences
gbenv Environmental sampling
gbest EST (expressed sequence tag)
gbgss GSS (genome survey sequence)
gbhtc HTC (high throughput cDNA sequencing)
gbhtg HTG (high throughput genomic sequencing)
gbinv Invertebrate
gbmam Other mammalian
gbpat Patent
gbphg Phage
gbpln Plant (including fungi and algae)
gbpri Primate
gbrod Rodent
gbsts STS (sequence tagged site)
gbsyn Synthetic and chimeric
gbtsa Transcriptome shotgun assembly
gbuna Unannotated
gbvrl Viral
gbvrt Other vertebrate

Genitalium
Version -
Date of preparation 17 Mar 2012 09:08
Description Mycoplasma genitalium G-37, complete genome
Origin (ftp) ftp.ncbi.nih.gov
Updates frequency variable
Other informations http://www.ncbi.nlm.nih.gov/genome/474?project_id=97
Sections genitalium full bank

Genpept
Version 187.0
Date of preparation 4 Apr 2012 23:07
Description Translations of Genbank
Origin (ftp) ftp.ncifcrf.gov
Updates frequency daily
Other informations ftp://ftp.ncifcrf.gov/pub/genpept/
Sections genpept_new updates
genpept release + updates
gpbct Bacterial
gpenv Environmental sampling
gpgss GSS (genome survey sequence)
gphtc HTC (high throughput cDNA sequencing)
gphtg HTG (high throughput genomic sequencing)
gpinv Invertebrate
gpmam Other mammalian
gppat Patent
gpphg Phage
gppln Plant (including fungi and algae)
gppri Primate
gprod Rodent
gpsts STS (sequence tagged site)
gpsyn Synthetic and chimeric
gpuna Unannotated
gpvrl Viral
gpvrt Other vertebrate

Hpylori
Version -
Date of preparation 17 Mar 2012 13:22
Description Helicobacter pylori 26695, complete genome
Origin (ftp) ftp.ncbi.nih.gov
Updates frequency variable
Other informations http://www.ncbi.nlm.nih.gov/genome/169?project_id=233
Sections hpylori full bank

Hssp
Version -
Date of preparation 6 Apr 2012 17:52
Description Homology-derived secondary structure of proteins database
Origin (ftp) ftp.cmbi.kun.nl
Updates frequency variable
Other informations ftp://ftp.ebi.ac.uk/pub/help/hssp.help

Imgt
Version 201147-6
Date of preparation 17 Mar 2012 15:11
Description IMGT/LIGM-DB, ImMunoGeneTics sequence database
Origin (ftp) ftp.cines.fr
Updates frequency weekly
Other informations http://www.imgt.org
Sections imgt full bank

Jaspar
Version -
Date of preparation 24 Jul 2009 15:39
Description High-quality transcription factor binding profile database
Origin (ftp) -
Updates frequency unknown
Other informations http://jaspar.genereg.net/

Mtuberculosis
Version -
Date of preparation 17 Mar 2012 15:12
Description Mycobacterium tuberculosis H37Rv, complete genome
Origin (ftp) ftp.ncbi.nih.gov
Updates frequency variable
Other informations http://www.ncbi.nlm.nih.gov/genome/166?project_id=224
Sections mtuberculosis full bank

Nrprot
Version 04.6
Date of preparation 4 Apr 2012 13:20
Description NCBI non-redundant: (Genbank CDS translations+PDB+Swissprot+PIR)
Origin (ftp) ftp.ncbi.nih.gov
Updates frequency monthly
Other informations http://www.ncbi.nlm.nih.gov/mapview/
Sections nrprot_new monthly updates
nrprot full bank

Nt
Version -
Date of preparation 5 Apr 2012 11:57
Description Nucleotide sequence database, minimally non-redundant
Origin (ftp) ftp.ncbi.nih.gov
Updates frequency variable
Other informations
Sections nt Nucleic sequences

Pdb
Version -
Date of preparation 5 Apr 2012 15:48
Description RCSB Protein Databank
Origin (ftp) rsync.wwpdb.org
Updates frequency daily
Other informations http://www.rcsb.org/pdb/

Pfam
Version 26.0
Date of preparation 5 Apr 2012 16:50
Description Collection of Protein Domain Families
Origin (ftp) ftp.sanger.ac.uk
Updates frequency variable
Other informations http://www.sanger.ac.uk/Pfam/

Pneumoniae
Version -
Date of preparation 17 Mar 2012 16:25
Description Mycoplasma pneumoniae M129, complete genome
Origin (ftp) ftp.ncbi.nih.gov
Updates frequency variable
Other informations http://www.ncbi.nlm.nih.gov/genome/1028?project_id=57709
Sections pneumoniae full bank

Prints
Version 41.1
Date of preparation 30 Mar 2011 15:53
Description Protein Motif Fingerprint Database
Origin (ftp) ftp.ebi.ac.uk
Updates frequency variable
Other informations http://www.biochem.ucl.ac.uk/bsm/dbbrowser/PRINTS/
Sections prints full bank

Prosite
Version 20.79
Date of preparation 26 Jan 2012 01:51
Description Dictionary of Protein Sites and Patterns
Origin (ftp) ftp.expasy.ch
Updates frequency variable
Other informations http://www.expasy.ch/prosite/
Sections prosite full bank

RDPII
Version 10_28
Date of preparation 5 Apr 2012 13:42
Description Ribosomal Database Project II database
Origin (ftp) -
Updates frequency monthly
Other informations http://rdp.cme.msu.edu/

Rebase
Version 204
Date of preparation 5 Apr 2012 13:50
Description The Restriction Enzyme Database
Origin (ftp) ftp.neb.com
Updates frequency variable
Other informations http://rebase.neb.com/rebase/rebase.html
Sections rebase full bank

RefSeq
Version 52
Date of preparation 20 Mar 2012 17:48
Description NCBI Reference Sequence (RefSeq) Database
Origin (ftp) ftp.ncbi.nih.gov
Updates frequency bimonthly
Other informations ftp://ftp.ncbi.nih.gov/refseq/README
Sections refseqn Nucleic sequences
refseqp Protein sequences

Taxodb
Version -
Date of preparation 31 Jan 2012 04:51
Description Taxonomy database
Origin (ftp) ftp.ncbi.nih.gov
Updates frequency daily
Other informations http://www.ncbi.nlm.nih.gov/guide/taxonomy/
Sections taxonomy full bank

UFMG
Version -
Date of preparation 20 Mar 2012 09:56
Description UnFinished Microbial Genomes (UFMG)
Origin (ftp) ftp.tigr.org
Updates frequency variable
Other informations
Sections ufmg full bank

Uniprot
Version 2012_03
Date of preparation 4 Apr 2012 09:09
Description Universal Protein Resource = SwissProt + TrEMBL + PIR
Origin (ftp) ftp.expasy.ch
Updates frequency weekly
Other informations http://www.expasy.org/sprot/
Sections uniprot full bank
uniprot_sprot SwissProt part
uniprot_trembl Trembl part

UniRef90
Version -
Date of preparation 20 Mar 2012 14:19
Description Clustered sets of sequences from UniProt Knowledgebase
Origin (ftp) ftp.expasy.ch
Updates frequency every
Other informations http://www.uniprot.org/help/uniref

Vector
Version -
Date of preparation 20 Mar 2012 13:40
Description Vector subset of GenBank(R), NCBI
Origin (ftp) ftp.ncbi.nih.gov
Updates frequency variable
Other informations http://www.ncbi.nlm.nih.gov/mapview/
Sections vector full bank

WGS
Version -
Date of preparation 21 Mar 2012 10:00
Description Genbank - Whole Genome Shotgun
Origin (ftp) ftp.ncbi.nih.gov
Updates frequency unknown
Other informations http://www.ncbi.nlm.nih.gov/Genbank/wgs.html
Sections wgsnuc Nucleic sequences
wgspro Protein sequences

Yeast
Version -
Date of preparation 20 Mar 2012 15:15
Description Yeast chromosomes
Origin (ftp) -
Updates frequency variable
Other informations http://www.yeastgenome.org/
Sections yeast full bank

Ypestis
Version -
Date of preparation 20 Mar 2012 15:15
Description Yersinia pestis unfinished genome
Origin (ftp) ftp.ncbi.nih.gov
Updates frequency variable
Other informations http://www.sanger.ac.uk/Projects/Y_pestis/
Sections ypestis full bank
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