Difference between revisions of "GFF source methods"

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(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...)
 
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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.

eg cyk in WormBase

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.