Difference between revisions of "Genome projects"
From Christoph's Personal Wiki
(→Mammals) |
|||
| (18 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
| + | *[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== | ||
| + | *[http://www.ncbi.nlm.nih.gov/genomes/static/gpstat.html NCBI - Genome sequencing projects statistics] | ||
*[http://www.ncbi.nlm.nih.gov/sites/entrez?db=Genome NCBI - All Genomes] | *[http://www.ncbi.nlm.nih.gov/sites/entrez?db=Genome NCBI - All Genomes] | ||
*[http://www.genomics.ceh.ac.uk/plasmiddb/plasmidview.html Plasmid Genome Database] (PGD) | *[http://www.genomics.ceh.ac.uk/plasmiddb/plasmidview.html Plasmid Genome Database] (PGD) | ||
*[http://www.ncbi.nlm.nih.gov/genomes/static/o.html NCBI - All plasmids] | *[http://www.ncbi.nlm.nih.gov/genomes/static/o.html NCBI - All plasmids] | ||
| + | *[http://www.ebi.ac.uk/genomes/plasmid.html Genomes Pages - Plasmid] — EMBL-EBI | ||
| + | *[http://www.ebi.ac.uk/genomes/organelle.html Genomes Pages - Organelle (including mitochondria)] — EMBL-EBI | ||
| + | *[http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj NCBI Entrez Genome Project Database] | ||
| + | *[http://www.genomesonline.org/ Genomes OnLine Database (GOLD)] | ||
| + | *[http://www.pseudogene.org/ Pseudogene.org] | ||
| + | |||
| + | ==List of genome project websites== | ||
| + | *[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] — 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] — 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)] — release: '''MGI 3.54''' (2008-01-19); mm3 (2003-02) | ||
| + | *[http://rgd.mcw.edu/ Rat Genome Database (RGD)] — 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 13: | Line 67: | ||
*[http://www.arabidopsis.org/ ''Arabidopsis''] | *[http://www.arabidopsis.org/ ''Arabidopsis''] | ||
*[http://www.yeastgenome.org/ SGD] — Yeast genome | *[http://www.yeastgenome.org/ SGD] — Yeast genome | ||
| − | |||
| − | |||
*[http://dictybase.org/ dictyBase] — resource for the biology and genomics of the social amoeba ''Dictyostelium discoideum''. | *[http://dictybase.org/ dictyBase] — 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.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://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://psychro.bioinformatics.unsw.edu.au/ Extremophiles] | *[http://psychro.bioinformatics.unsw.edu.au/ Extremophiles] | ||
| − | |||
*[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 38: | Line 86: | ||
*[http://www.toxodb.org/ ''Toxoplasma''] | *[http://www.toxodb.org/ ''Toxoplasma''] | ||
*[http://cryptodb.org/ ''Cryptosporidium''] | *[http://cryptodb.org/ ''Cryptosporidium''] | ||
| − | |||
*[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:// | + | *[http://www.bacterio.cict.fr/ List of Prokaryotic names with Standing in Nomenclature] |
==Databases== | ==Databases== | ||
| Line 54: | Line 111: | ||
*[http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/printscontents.html PRINTS] | *[http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/printscontents.html PRINTS] | ||
*[http://www.bioinf.manchester.ac.uk/dbbrowser/ALIGN/ ALIGN] | *[http://www.bioinf.manchester.ac.uk/dbbrowser/ALIGN/ ALIGN] | ||
| + | *[http://www.methdb.net/ MethDB: DNA Methylation Database] | ||
| + | *[http://chromdb.org/ ChromDB::Chromatin Database] | ||
| + | *[http://www.genenames.org/ GeneNames.org] — by the HUGO Gene Nomenclature Committee (HGNC) | ||
| + | *[http://insilico.ehu.es/oligoweb/index2.php?m=all Nucleotide and oligonucleotide composition of genomes] — for all currently sequenced prokaryote genomes. | ||
| + | |||
| + | ==Other== | ||
| + | *[http://microbewiki.kenyon.edu/index.php/MicrobeWiki MicrobeWiki] | ||
[[Category:Bioinformatics]] | [[Category:Bioinformatics]] | ||
Latest revision as of 20:08, 7 August 2012
Contents
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
- NCBI - Genome sequencing projects statistics
- NCBI - All Genomes
- Plasmid Genome Database (PGD)
- NCBI - All plasmids
- Genomes Pages - Plasmid — EMBL-EBI
- Genomes Pages - Organelle (including mitochondria) — EMBL-EBI
- NCBI Entrez Genome Project Database
- Genomes OnLine Database (GOLD)
- Pseudogene.org
List of genome project websites
- UCSC Genome Bioinformatics Site
- BioCyc — a collection of 260 Pathway/Genome Databases
- GeneDB at WT Sanger Institute including S. pombe
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
- UCSC Human Genome — release: hg19; GRCh37 genebuild (March 2009)
- 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).
- James Watson's genome — on TraceDB/Personal Genomics (NCBI)
- Human HapMap
- Human Genome Segmental Duplication Database
- Mouse Genome Informatics (MGI) — release: MGI 3.54 (2008-01-19); mm3 (2003-02)
- Rat Genome Database (RGD) — release: RGD 3.4; rn3 (2003-06)
Other
- FishBase
- FlyBase
- wFleaBase
- WormBase — C. elegans genome, C. briggsae genome, etc.
- BeeBase — the Apis mellifera genome.
- Gramene
- Arabidopsis
- SGD — Yeast genome
- dictyBase — resource for the biology and genomics of the social amoeba Dictyostelium discoideum.
- EcoliHub / The E. coli Wiki
- Nescent.org
- Saccharomyces Genome Database
- Dictybase
- Fungal Genome Database
- Paramecium DB
- Bradyrhizobium japonicum USDA 110 (NCBI)
- Extremophiles
- OryGenesDB
- Pseudomonas
- Tribolium (Beetle)
- Tetrahymena
- Marine Biological Lab projects including Giardia, Trypanosome brucei, and many others
- Solonaceae Genome Network
- Maize Genome Database (MIPS)
- Maize Genome Assembly
- Toxoplasma
- Cryptosporidium
- Marine Roseobacters
- Rice-Magnaporthe interaction database
- Candida Genome Database
- GrainGenes: Triticeae and Avena
- Aniseed Genome Browser
Viruses
- International Committee on Taxonomy of Viruses (ICTVdb)
- wikipedia:International Committee on Taxonomy of Viruses
- wikipedia:Mimivirus (Acanthamoeba polyphaga mimivirus (APMV))
- wikipedia:Nanoarchaeum equitans
- poxvirus.org (PBR)
- Viral Bioinformatics Resource Center
Related
Databases
- http://ecoliwiki.net/colipedia/index.php/Category:Databases
- African Mammals Databank
- TreeBASE — a relational database of phylogenetic information
- PROSITE — database of protein domains, families, and functional sites
- PRINTS
- ALIGN
- MethDB: DNA Methylation Database
- ChromDB::Chromatin Database
- GeneNames.org — by the HUGO Gene Nomenclature Committee (HGNC)
- Nucleotide and oligonucleotide composition of genomes — for all currently sequenced prokaryote genomes.
