Difference between revisions of "Genome projects"
From Christoph's Personal Wiki
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*[http://www.biocyc.org/ BioCyc] — a collection of 260 Pathway/Genome Databases | *[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''] | *[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=== | ===Mammals=== | ||
| − | *[http://genome.ucsc.edu/ENCODE/ UCSC Human Genome] — release: '''hg18''' (2006-03) | + | *[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) | *[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://www.hapmap.org/ Human HapMap] | ||
| Line 31: | Line 57: | ||
*[http://www.informatics.jax.org/ Mouse Genome Informatics (MGI)] — release: '''MGI 3.54''' (2008-01-19); mm3 (2003-02) | *[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) | *[http://rgd.mcw.edu/ Rat Genome Database (RGD)] — release: '''RGD 3.4'''; rn3 (2003-06) | ||
| + | |||
===Other=== | ===Other=== | ||
*[http://www.fishbase.org/search.php FishBase] | *[http://www.fishbase.org/search.php FishBase] | ||
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.
