Difference between revisions of "Genome projects"
From Christoph's Personal Wiki
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==List of genome project websites== | ==List of genome project websites== | ||
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*[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''] | ||
| + | ===Mammals=== | ||
| + | *[http://genome.ucsc.edu/ENCODE/ UCSC Human Genome] — release: '''hg18''' (2006-03) | ||
| + | *[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] | ||
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*[http://www.arabidopsis.org/ ''Arabidopsis''] | *[http://www.arabidopsis.org/ ''Arabidopsis''] | ||
*[http://www.yeastgenome.org/ SGD] — Yeast genome | *[http://www.yeastgenome.org/ SGD] — Yeast genome | ||
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*[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] | ||
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*[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] | ||
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*[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] | ||
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*[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''] | ||
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*[http://www.toxodb.org/ ''Toxoplasma''] | *[http://www.toxodb.org/ ''Toxoplasma''] | ||
*[http://cryptodb.org/ ''Cryptosporidium''] | *[http://cryptodb.org/ ''Cryptosporidium''] | ||
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*[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] | ||
| + | ===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] | ||
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==Databases== | ==Databases== | ||
Revision as of 06:47, 22 January 2008
Contents
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
Mammals
- UCSC Human Genome — release: hg18 (2006-03)
- 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
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.
