Difference between revisions of "Reference Genome sequence annotation (Retired)"

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|[http://www.dictybase.org dictyBase]
|[http://www.dictybase.org dictyBase]
|updated weekly
|Arabidopsis thaliana
|Arabidopsis thaliana

Revision as of 10:22, 18 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. ( * means that the presented file is not yet SO compliant)
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 updated weekly
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 * ftp://ftp.ensembl.org/pub/current_homo_sapiens/data/gtf/ ?
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 ? ?

Nota bene

  1. The human data is in GTF (not GFF3)
  2. 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