Difference between revisions of "Genome projects"

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==List of active genome projects==
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*[http://www.genomenewsnetwork.org/ Genome News Network]
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==Statistics==
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[http://www.ncbi.nlm.nih.gov/genome/browse/ Total genomes sequenced], as of 27-Jul-2012:
 +
* Eukaryotes: 2,017
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* Prokaryotes: 13,054
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* Viruses: 3,155
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 +
see: [ftp://ftp.ncbi.nih.gov/genomes/Bacteria/ directory] for a daily updated list of completed microbial genomes.
 +
 
 +
==List overviews==
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*[http://www.ncbi.nlm.nih.gov/genomes/static/gpstat.html NCBI - Genome sequencing projects statistics]
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*[http://www.ncbi.nlm.nih.gov/sites/entrez?db=Genome NCBI - All Genomes]
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*[http://www.genomics.ceh.ac.uk/plasmiddb/plasmidview.html Plasmid Genome Database] (PGD)
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*[http://www.ncbi.nlm.nih.gov/genomes/static/o.html NCBI - All plasmids]
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*[http://www.ebi.ac.uk/genomes/plasmid.html Genomes Pages - Plasmid] — EMBL-EBI
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*[http://www.ebi.ac.uk/genomes/organelle.html Genomes Pages - Organelle (including mitochondria)] — EMBL-EBI
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*[http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj NCBI Entrez Genome Project Database]
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*[http://www.genomesonline.org/ Genomes OnLine Database (GOLD)]
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*[http://www.pseudogene.org/ Pseudogene.org]
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==List of genome project websites==
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*[http://genome.ucsc.edu/ UCSC Genome Bioinformatics Site]
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*[http://www.biocyc.org/ BioCyc] — a collection of 260 Pathway/Genome Databases
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*[http://www.genedb.org GeneDB] at [http://www.sanger.ac.uk WT Sanger Institute] including [http://www.genedb.org/genedb/pombe/ ''S. pombe'']
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===Personal Genomes sequenced by date===
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see: [http://personalgenomics.org/index.php/Main_Page PersonalGenomics.org]
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* Craig Venter: 2007-09-04
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* James Watson: 2008-04-09
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* Yang Huanming: 2008-10-17
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* Seong-Jin Kim: 2008-12-04
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* Misha Angrist: 2009-03-31
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* Rosalynn Gill: 2009-03-31
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* Jay Flatley: 2009-05-20
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* Henry Louis "Skip" Gates Jr.: 2009-08-10
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* Hermann Hauser: 2009-08-20
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* Henry Louis Gates Sr.: 2009-08-21
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* George Church: 2009-11-05
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* Glenn Close: 2009-11-20
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* John West: 2010-01-25
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* Judy West: 2010-01-25
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* Anne West: 2010-01-25
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* Paul West: 2010-01-25
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* Desmond Tutu: 2010-02-17
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* James Lupski: 2010-03-10
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* Rosalyn Gill: 2010-04-20
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* Stephen Quake: 2010-04-30
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* Greg Lucier: 2010-05-01
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===Mammals===
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*[http://genome.ucsc.edu/ENCODE/ UCSC Human Genome] &mdash; release: '''hg19'''; GRCh37 genebuild (March 2009)<!-- '''hg18''' (2006-03)--->
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*:NCBI reference Build 37, which consists of the assembled nuclear chromosome from GRCh37 plus the Cambridge Reference Sequence for the mitochondrion (NC_012920.1). This assembly is also known as UCSC hg19 (though with an alternate mitochondrial sequence).
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*[ftp://ftp.ncbi.nih.gov/pub/TraceDB/Personal_Genomics/ James Watson's genome] &mdash; on TraceDB/Personal Genomics (NCBI)
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*[http://www.hapmap.org/ Human HapMap]
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*[http://projects.tcag.ca/cgi-bin/duplication/dupbrowse/human_b35 Human Genome Segmental Duplication Database]
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*[http://www.informatics.jax.org/ Mouse Genome Informatics (MGI)] &mdash; release: '''MGI 3.54''' (2008-01-19); mm3 (2003-02)
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*[http://rgd.mcw.edu/ Rat Genome Database (RGD)] &mdash; release: '''RGD 3.4'''; rn3 (2003-06)
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===Other===
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*[http://www.fishbase.org/search.php FishBase]
 
*[http://www.flybase.org/ FlyBase]
 
*[http://www.flybase.org/ FlyBase]
 
*[http://wfleabase.org/ wFleaBase]
 
*[http://wfleabase.org/ wFleaBase]
 
*[http://www.wormbase.org/ WormBase] &mdash; ''C. elegans'' genome, ''C. briggsae'' genome, etc.
 
*[http://www.wormbase.org/ WormBase] &mdash; ''C. elegans'' genome, ''C. briggsae'' genome, etc.
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*[http://racerx00.tamu.edu/bee_resources.html BeeBase] &mdash; the ''Apis mellifera'' genome.
 
*[http://www.gramene.org/ Gramene]
 
*[http://www.gramene.org/ Gramene]
 
*[http://www.arabidopsis.org/ ''Arabidopsis'']
 
*[http://www.arabidopsis.org/ ''Arabidopsis'']
 
*[http://www.yeastgenome.org/ SGD] &mdash; Yeast genome
 
*[http://www.yeastgenome.org/ SGD] &mdash; Yeast genome
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*[http://www.informatics.jax.org/ Mouse Genome Informatics (MGI)]
 
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*[http://rgd.mcw.edu/ The Rat Genome Database (RGD)]
 
 
*[http://dictybase.org/ dictyBase] &mdash; resource for the biology and genomics of the social amoeba ''Dictyostelium discoideum''.
 
*[http://dictybase.org/ dictyBase] &mdash; resource for the biology and genomics of the social amoeba ''Dictyostelium discoideum''.
 
*[http://ecolihub.org/ EcoliHub] / [http://ecoliwiki.net/colipedia/index.php/Main_Page The ''E. coli'' Wiki]
 
*[http://ecolihub.org/ EcoliHub] / [http://ecoliwiki.net/colipedia/index.php/Main_Page The ''E. coli'' Wiki]
 
*[http://www.nescent.org/ Nescent.org]
 
*[http://www.nescent.org/ Nescent.org]
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*[http://www.biocyc.org/ BioCyc] &mdash; a collection of 260 Pathway/Genome Databases
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*[http://www.yeastgenome.org ''Saccharomyces'' Genome Database]
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*[http://dictybase.org/ Dictybase]
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*[http://fungal.genome.duke.edu Fungal Genome Database]
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*[http://paramecium.cgm.cnrs-gif.fr/db/index ''Paramecium'' DB]
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*[http://www.bradygenome.org/ ''Bradyrhizobium japonicum'' USDA 110] ([http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=17 NCBI])
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*[http://psychro.bioinformatics.unsw.edu.au/ Extremophiles]
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*[http://orygenesdb.cines.fr/cgi-bin/gbrowse/orygenesdb OryGenesDB]
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*[http://v2.pseudomonas.com/ ''Pseudomonas'']
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*[http://www.bioinformatics.ksu.edu/BeetleBase/index.shtml ''Tribolium'' (Beetle)]
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*[http://www.ciliate.org/ ''Tetrahymena'']
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*[http://gmod.mbl.edu Marine Biological Lab] projects including [http://www.mbl.edu/Giardia ''Giardia''], [http://gmod.mbl.edu/perl/site/t_bruceibrucei02 ''Trypanosome brucei''], and many others
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*[http://www.sgn.cornell.edu/ ''Solonaceae'' Genome Network]
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*[http://mips.gsf.de/proj/plant/jsf/maize/index.jsp Maize Genome Database] (MIPS)
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*[http://magi.plantgenomics.iastate.edu/ Maize Genome Assembly]
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*[http://www.toxodb.org/ ''Toxoplasma'']
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*[http://cryptodb.org/ ''Cryptosporidium'']
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*[http://roseobase.org/ Marine ''Roseobacters'']
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*[http://www.mgosdb.org/ Rice-Magnaporthe interaction database]
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*[http://www.candidagenome.org/ Candida Genome Database]
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*[http://wheat.pw.usda.gov/ GrainGenes: ''Triticeae'' and ''Avena'']
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*[http://crfb.univ-mrs.fr/ciona-bin/gbrowse/intestinalis/ Aniseed Genome Browser]
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===Viruses===
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*[http://phene.cpmc.columbia.edu/Ictv/index.htm International Committee on Taxonomy of Viruses] (ICTVdb)
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*[[wikipedia:International Committee on Taxonomy of Viruses]]
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*[[wikipedia:Mimivirus]] (''Acanthamoeba polyphaga mimivirus'' (APMV))
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*''[[wikipedia:Nanoarchaeum equitans]]''
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*[http://www.poxvirus.org/ poxvirus.org (PBR)]
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*[http://athena.bioc.uvic.ca/workbench.php?tool=vgo Viral Bioinformatics Resource Center]
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===Related===
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*[http://t1dbase.org Type I Diabetes]
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*[http://www.biohealthbase.org/GSearch/ Biohealthbase]
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*[http://www.bacterio.cict.fr/ List of Prokaryotic names with Standing in Nomenclature]
  
 
==Databases==
 
==Databases==
 
*http://ecoliwiki.net/colipedia/index.php/Category:Databases
 
*http://ecoliwiki.net/colipedia/index.php/Category:Databases
 +
*[http://www.fishbase.org/search.php African Mammals Databank]
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*[http://www.treebase.org/treebase/index.html TreeBASE] &mdash; a relational database of phylogenetic information
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*[http://www.expasy.ch/prosite/ PROSITE] &mdash; database of protein domains, families, and functional sites
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*[http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/printscontents.html PRINTS]
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*[http://www.bioinf.manchester.ac.uk/dbbrowser/ALIGN/ ALIGN]
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*[http://www.methdb.net/ MethDB: DNA Methylation Database]
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*[http://chromdb.org/ ChromDB::Chromatin Database]
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*[http://www.genenames.org/ GeneNames.org] &mdash; by the HUGO Gene Nomenclature Committee (HGNC)
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*[http://insilico.ehu.es/oligoweb/index2.php?m=all Nucleotide and oligonucleotide composition of genomes] &mdash; for all currently sequenced prokaryote genomes.
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 +
==Other==
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*[http://microbewiki.kenyon.edu/index.php/MicrobeWiki MicrobeWiki]
  
 
[[Category:Bioinformatics]]
 
[[Category:Bioinformatics]]

Latest revision as of 20:08, 7 August 2012

Statistics

Total genomes sequenced, as of 27-Jul-2012:

  • Eukaryotes: 2,017
  • Prokaryotes: 13,054
  • Viruses: 3,155
see: directory for a daily updated list of completed microbial genomes.

List overviews

List of genome project websites

Personal Genomes sequenced by date

see: PersonalGenomics.org
  • Craig Venter: 2007-09-04
  • James Watson: 2008-04-09
  • Yang Huanming: 2008-10-17
  • Seong-Jin Kim: 2008-12-04
  • Misha Angrist: 2009-03-31
  • Rosalynn Gill: 2009-03-31
  • Jay Flatley: 2009-05-20
  • Henry Louis "Skip" Gates Jr.: 2009-08-10
  • Hermann Hauser: 2009-08-20
  • Henry Louis Gates Sr.: 2009-08-21
  • George Church: 2009-11-05
  • Glenn Close: 2009-11-20
  • John West: 2010-01-25
  • Judy West: 2010-01-25
  • Anne West: 2010-01-25
  • Paul West: 2010-01-25
  • Desmond Tutu: 2010-02-17
  • James Lupski: 2010-03-10
  • Rosalyn Gill: 2010-04-20
  • Stephen Quake: 2010-04-30
  • Greg Lucier: 2010-05-01

Mammals

Other

Viruses

Related

Databases

Other

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