Reference Genome sequence annotation (Retired): Difference between revisions

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The Reference Genome initiative will foster [http://www.sequenceontology.org SO] compliant annotations. The sequences will be available using the file format  [http://www.sequenceontology.org/gff3.shtml GFF3].
The Reference Genome initiative will foster [http://www.sequenceontology.org SO] compliant annotations. The sequences will be available using the file format  [http://www.sequenceontology.org/gff3.shtml GFF3].


 
For discussion on standardizing URLs for accessing this information please see the GMOD wiki page
[http://www.gmod.org/wiki/index.php/Standard_URL Standard URL]


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Revision as of 16:43, 15 September 2007

The Reference Genome initiative will foster SO compliant annotations. The sequences will be available using the file format GFF3.

For discussion on standardizing URLs for accessing this information please see the GMOD wiki page Standard URL

Where to find SO compliant GFF3 annotations for the Reference Genome sequences.
Organism Organization Download Date
Drosophila melanogaster (Fruitfly) FlyBase ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff 9/12/07
Caenorhabditis elegans (Worm) WormBase ftp://ftp.wormbase.org/pub/wormbase/genomes/elegans/genome_feature_tables/GFF3 ?
Saccharomyces cerevisiae (Budding yeast) SGD ftp://genome-ftp.stanford.edu/pub/yeast/chromosomal_feature/saccharomyces_cerevisiae.gff ?
Dictyostelium (cellular slime mold) dictyBase http://www.dictybase.org/db/cgi-bin/dictyBase/download/download.pl?area=gff3&ID=dicty_gff3.zip ?
Arabidopsis thaliana TAIR ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR7_genome_release/TAIR7_gff3 8/15/07
Danio rerio (Zebrafish) ZFIN ? ?
Mouse MGI ? ?
Human GOA ? ?
Schizosaccharomyces pombe (Fission yeast) Sanger Centre ftp://ftp.sanger.ac.uk/pub/yeast/pombe/GFF/ 3/16/07
E.coli ASAP https://asap.ahabs.wisc.edu/asap/download_gff3.php?LocationID=&SequenceVersionID=&GenomeID= ?
Rat RGD ? ?