Difference between revisions of "GFF source methods"
From WormBaseWiki
Jump to navigationJump to search (New page: == GFF source and feature == [http://www.sanger.ac.uk/Software/formats/GFF/ GFF2 description at the Sanger Institute] In the WormBase GFF files genes are represented in several ways each...) |
|||
| Line 8: | Line 8: | ||
This is the largest extent of a genes' transcripts from the begining of the most 5' transcripts 5' UTR to the end of the most 3' transcripts 3' UTR. Each gene is represented as a single line. | This is the largest extent of a genes' transcripts from the begining of the most 5' transcripts 5' UTR to the end of the most 3' transcripts 3' UTR. Each gene is represented as a single line. | ||
| − | source = gene; feature = gene. | + | *source = '''gene'''; feature = '''gene'''. |
eg [http://www.wormbase.org/db/gene/gene?name=WBGene00000875;class=Gene cyk in WormBase] | eg [http://www.wormbase.org/db/gene/gene?name=WBGene00000875;class=Gene cyk in WormBase] | ||
| − | CHROMOSOME_III gene gene 13768424 13771124 . - . Gene WBGene00000875" ; Position "21.5305" ; Locus "cyk-4" | + | |
| + | CHROMOSOME_III '''gene gene''' 13768424 13771124 . - . Gene WBGene00000875" ; Position "21.5305" ; Locus "cyk-4" | ||
| + | |||
| + | |||
| + | === CDS === | ||
| + | A CDS is the coding sequence of a gene from the start codon to the stop codon (so does not include UTR). A gene may have 1 or more CDS's. | ||
Revision as of 11:05, 21 April 2009
GFF source and feature
GFF2 description at the Sanger Institute
In the WormBase GFF files genes are represented in several ways each specified by a different source and feature (second and third columns)
Gene spans
This is the largest extent of a genes' transcripts from the begining of the most 5' transcripts 5' UTR to the end of the most 3' transcripts 3' UTR. Each gene is represented as a single line.
- source = gene; feature = gene.
CHROMOSOME_III gene gene 13768424 13771124 . - . Gene WBGene00000875" ; Position "21.5305" ; Locus "cyk-4"
CDS
A CDS is the coding sequence of a gene from the start codon to the stop codon (so does not include UTR). A gene may have 1 or more CDS's.
