Difference between revisions of "Genome projects"

From Christoph's Personal Wiki
Jump to: navigation, search
(Databases)
(Mammals)
 
(8 intermediate revisions by the same user not shown)
Line 1: Line 1:
 
*[http://www.genomenewsnetwork.org/ Genome News Network]
 
*[http://www.genomenewsnetwork.org/ Genome News Network]
 +
 +
==Statistics==
 +
[http://www.ncbi.nlm.nih.gov/genome/browse/ Total genomes sequenced], as of 27-Jul-2012:
 +
* Eukaryotes: 2,017
 +
* Prokaryotes: 13,054
 +
* Viruses: 3,155
 +
 +
see: [ftp://ftp.ncbi.nih.gov/genomes/Bacteria/ directory] for a daily updated list of completed microbial genomes.
  
 
==List overviews==
 
==List overviews==
Line 13: Line 21:
  
 
==List of genome project websites==
 
==List of genome project websites==
*[ftp://ftp.ncbi.nih.gov/pub/TraceDB/Personal_Genomics/ James Watson's genome] — on TraceDB/Personal Genomics (NCBI)
 
 
*[http://genome.ucsc.edu/ UCSC Genome Bioinformatics Site]
 
*[http://genome.ucsc.edu/ UCSC Genome Bioinformatics Site]
 +
*[http://www.biocyc.org/ BioCyc] — a collection of 260 Pathway/Genome Databases
 +
*[http://www.genedb.org GeneDB] at [http://www.sanger.ac.uk WT Sanger Institute] including [http://www.genedb.org/genedb/pombe/ ''S. pombe'']
 +
 +
===Personal Genomes sequenced by date===
 +
see: [http://personalgenomics.org/index.php/Main_Page 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===
 +
*[http://genome.ucsc.edu/ENCODE/ UCSC Human Genome] &mdash; release: '''hg19'''; GRCh37 genebuild (March 2009)<!-- '''hg18''' (2006-03)--->
 +
*: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).
 +
*[ftp://ftp.ncbi.nih.gov/pub/TraceDB/Personal_Genomics/ James Watson's genome] &mdash; on TraceDB/Personal Genomics (NCBI)
 +
*[http://www.hapmap.org/ Human HapMap]
 +
*[http://projects.tcag.ca/cgi-bin/duplication/dupbrowse/human_b35 Human Genome Segmental Duplication Database]
 +
*[http://www.informatics.jax.org/ Mouse Genome Informatics (MGI)] &mdash; release: '''MGI 3.54''' (2008-01-19); mm3 (2003-02)
 +
*[http://rgd.mcw.edu/ Rat Genome Database (RGD)] &mdash; release: '''RGD 3.4'''; rn3 (2003-06)
 +
 +
===Other===
 
*[http://www.fishbase.org/search.php FishBase]
 
*[http://www.fishbase.org/search.php FishBase]
 
*[http://www.flybase.org/ FlyBase]
 
*[http://www.flybase.org/ FlyBase]
Line 23: Line 67:
 
*[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
*[http://www.informatics.jax.org/ Mouse Genome Informatics (MGI)]
 
*[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]
*[http://www.biocyc.org/ BioCyc] &mdash; a collection of 260 Pathway/Genome Databases
 
*[http://projects.tcag.ca/cgi-bin/duplication/dupbrowse/human_b35 Human Genome Segmental Duplication Database]
 
 
*[http://www.yeastgenome.org ''Saccharomyces'' Genome Database]
 
*[http://www.yeastgenome.org ''Saccharomyces'' Genome Database]
 
*[http://dictybase.org/ Dictybase]
 
*[http://dictybase.org/ Dictybase]
 
*[http://fungal.genome.duke.edu Fungal Genome Database]
 
*[http://fungal.genome.duke.edu Fungal Genome Database]
*[http://www.informatics.jax.org/ Mouse Genome Informatics]
 
*[http://rgd.mcw.edu/ Rat Genome Database]
 
 
*[http://paramecium.cgm.cnrs-gif.fr/db/index ''Paramecium'' DB]
 
*[http://paramecium.cgm.cnrs-gif.fr/db/index ''Paramecium'' DB]
 
*[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])
 
*[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])
 
*[http://psychro.bioinformatics.unsw.edu.au/ Extremophiles]
 
*[http://psychro.bioinformatics.unsw.edu.au/ Extremophiles]
*[http://www.hapmap.org/ Human HapMap]
 
 
*[http://orygenesdb.cines.fr/cgi-bin/gbrowse/orygenesdb OryGenesDB]
 
*[http://orygenesdb.cines.fr/cgi-bin/gbrowse/orygenesdb OryGenesDB]
 
*[http://v2.pseudomonas.com/ ''Pseudomonas'']
 
*[http://v2.pseudomonas.com/ ''Pseudomonas'']
Line 49: Line 86:
 
*[http://www.toxodb.org/ ''Toxoplasma'']
 
*[http://www.toxodb.org/ ''Toxoplasma'']
 
*[http://cryptodb.org/ ''Cryptosporidium'']
 
*[http://cryptodb.org/ ''Cryptosporidium'']
*[http://www.genedb.org GeneDB] at [http://www.sanger.ac.uk WT Sanger Institute] including [http://www.genedb.org/genedb/pombe/ ''S. pombe'']
 
 
*[http://roseobase.org/ Marine ''Roseobacters'']
 
*[http://roseobase.org/ Marine ''Roseobacters'']
 
*[http://www.mgosdb.org/ Rice-Magnaporthe interaction database]
 
*[http://www.mgosdb.org/ Rice-Magnaporthe interaction database]
 
*[http://www.candidagenome.org/ Candida Genome Database]
 
*[http://www.candidagenome.org/ Candida Genome Database]
 
*[http://wheat.pw.usda.gov/ GrainGenes: ''Triticeae'' and ''Avena'']
 
*[http://wheat.pw.usda.gov/ GrainGenes: ''Triticeae'' and ''Avena'']
 +
*[http://crfb.univ-mrs.fr/ciona-bin/gbrowse/intestinalis/ Aniseed Genome Browser]
 +
===Viruses===
 +
*[http://phene.cpmc.columbia.edu/Ictv/index.htm International Committee on Taxonomy of Viruses] (ICTVdb)
 +
*[[wikipedia:International Committee on Taxonomy of Viruses]]
 +
*[[wikipedia:Mimivirus]] (''Acanthamoeba polyphaga mimivirus'' (APMV))
 +
*''[[wikipedia:Nanoarchaeum equitans]]''
 +
*[http://www.poxvirus.org/ poxvirus.org (PBR)]
 +
*[http://athena.bioc.uvic.ca/workbench.php?tool=vgo Viral Bioinformatics Resource Center]
 +
 +
===Related===
 
*[http://t1dbase.org Type I Diabetes]
 
*[http://t1dbase.org Type I Diabetes]
 
*[http://www.biohealthbase.org/GSearch/ Biohealthbase]
 
*[http://www.biohealthbase.org/GSearch/ Biohealthbase]
*[http://crfb.univ-mrs.fr/ciona-bin/gbrowse/intestinalis/ Aniseed Genome Browser]
+
*[http://www.bacterio.cict.fr/ List of Prokaryotic names with Standing in Nomenclature]
  
 
==Databases==
 
==Databases==
Line 68: Line 114:
 
*[http://chromdb.org/ ChromDB::Chromatin Database]
 
*[http://chromdb.org/ ChromDB::Chromatin Database]
 
*[http://www.genenames.org/ GeneNames.org] &mdash; by the HUGO Gene Nomenclature Committee (HGNC)
 
*[http://www.genenames.org/ GeneNames.org] &mdash; by the HUGO Gene Nomenclature Committee (HGNC)
 +
*[http://insilico.ehu.es/oligoweb/index2.php?m=all Nucleotide and oligonucleotide composition of genomes] &mdash; for all currently sequenced prokaryote genomes.
  
 
==Other==
 
==Other==

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