Reference Genome sequence annotation (Retired)

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Revision as of 13:41, 12 November 2007 by Vpetri (talk | contribs) (→‎Nota bene)
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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. ( * means that the presented file is not yet SO compliant)
Organism Organization Download Date
Drosophila melanogaster (Fruitfly) FlyBase 9/12/07
Caenorhabditis elegans (Worm) WormBase ?
Saccharomyces cerevisiae (Budding yeast) SGD ?
Dictyostelium (cellular slime mold) dictyBase updated weekly
Arabidopsis thaliana TAIR 8/15/07
Danio rerio (Zebrafish) ZFIN Sanger Institute Vega:
With new releases
Mouse MGI ? ?
Human GOA ?
Schizosaccharomyces pombe (Fission yeast) Sanger Centre * 3/16/07
E.coli ASAP ?
Rat RGD ?

Nota bene

  1. The human and zebrafish Ensembl data is in GTF (not GFF3)
  2. The rat Ensembl data (link provided) is also in GTF format
  3. The pombe files are not (yet) valid GFF3. The known problems are:
    • extra column 10 "Name"
    • extra column 11 "orf_classification"
    • extra column 12 "gene"
    • extra column 13 "chr"
    • the mandatory "phase" column isn't filled in.
    • and the attributes" column may not be formatted correctly.

Back to: Reference_Genome_Focus