[maker-devel] Maker-derived CDS GFF3 phase column

[Carson Holt]

It looks like the phase was calculated from the wrong strand orientation.  I
believe I have corrected this now.  I'm checking a few more things, but I'll
have 2.28 as the latest release likely tomorrow with the cumulative bug
fixes since the last release.

Thanks,
Carson



From:  Rob Syme <rob.syme at gmail.com>
Date:  Tuesday, 21 May, 2013 1:57 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Maker-derived CDS GFF3 phase column

Hi all

By my reading of the GFF3 spec
(http://sequenceontology.org/resources/gff3.html), I'm getting gff3 from
Maker that has odd data in the phase column.

For example, see some example Maker output at
https://gist.github.com/robsyme/5617399

There are two exons, 5617 <- 5737 and 5793 <- 5953 with phases 0 and 2,
respectively. Both exons are in the reverse strand.

>From the spec, phase indicates "the number of bases that should be removed
from the beginning of this feature to reach the first base of the next
codon", and for "reverse strand features, phase is counted from the end
field". 

In the case of the 3' exon (5793 <- 5953), the end field (the 5th column) is
5953. 
The base at the end field is the first base of the translated CDS, so there
should be no bases removed "to reach the first base of the next codon". I
suggest that this phase should be 0, not 2.

There is an illustration of the feature at http://i.imgur.com/DKLxnSf.png.

The output gff3 is correct if "the number of bases that should be removed
from the beginning of this feature to reach the first base of the next
codon" is measured from the 'left-hand' end of this feature (the start
field) rather than the end field.

Has anybody else ran into this problem or am I misreading the gff3 spec?

Rob Syme
PhD Student
Curtin University




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