Reference Genome sequence annotation (Retired): Difference between revisions
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[[Category:PAINT Archived]] | |||
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]. | ||
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|[http://www.yeastgenome.org SGD] | |[http://www.yeastgenome.org SGD] | ||
|ftp://genome-ftp.stanford.edu/pub/yeast/chromosomal_feature/saccharomyces_cerevisiae.gff | |ftp://genome-ftp.stanford.edu/pub/yeast/chromosomal_feature/saccharomyces_cerevisiae.gff | ||
| | |updated nightly | ||
|- | |- | ||
|Dictyostelium (cellular slime mold) | |Dictyostelium (cellular slime mold) | ||
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|- | |- | ||
|Danio rerio (Zebrafish) | |Danio rerio (Zebrafish) | ||
|[http://zfin.org ZFIN] | |[http://zfin.org ZFIN] [http://www.sanger.ac.uk Sanger Institute] | ||
|Vega: ftp://ftp.sanger.ac.uk/pub/vega/danio/gff3/ | |Vega: ftp://ftp.sanger.ac.uk/pub/vega/danio/gff3/vega_danio_rerio_20070803.gff3 <br> Ensembl*: ftp://ftp.ensembl.org/pub/current_gtf/Danio_rerio.ZFISH7.47.gtf.gz | ||
|With new releases | |With new releases | ||
|- | |- | ||
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|Human | |Human | ||
|[http://www.ebi.ac.uk/GOA/ GOA] | |[http://www.ebi.ac.uk/GOA/ GOA] | ||
| | | ftp://ftp.ensembl.org/pub/current_gtf/Homo_sapiens.NCBI36.47.gtf.gz | ||
|? | |? | ||
|- | |- | ||
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|[http://www.sanger.ac.uk/Projects/S_pombe/ Sanger Centre] | |[http://www.sanger.ac.uk/Projects/S_pombe/ Sanger Centre] | ||
| * ftp://ftp.sanger.ac.uk/pub/yeast/pombe/GFF/ | | * ftp://ftp.sanger.ac.uk/pub/yeast/pombe/GFF/ | ||
| | |7/17/08 | ||
|- | |- | ||
|E.coli | |E.coli | ||
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|Rat | |Rat | ||
|[http://rgd.mcw.edu/ RGD] | |[http://rgd.mcw.edu/ RGD] | ||
| | |ftp://ftp.ensembl.org/pub/current_gtf/Rattus_norvegicus.RGSC3.4.47.gtf.gz | ||
|? | |? | ||
|- | |- | ||
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== Nota bene == | == Nota bene == | ||
# The human and zebrafish Ensembl data is in GTF (not GFF3) | # The human and zebrafish Ensembl data is in GTF (not GFF3) | ||
# The rat Ensembl data (link provided) is also in GTF format | |||
# The pombe files are not (yet) valid GFF3. The known problems are: | # The pombe files are not (yet) valid GFF3. The known problems are: | ||
#* extra column 10 "Name" | #* extra column 10 "Name" |
Latest revision as of 11:16, 12 April 2019
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
Nota bene
- The human and zebrafish Ensembl data is in GTF (not GFF3)
- The rat Ensembl data (link provided) is also in GTF format
- 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.
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