[maker-devel] Serious Start Codon Problem

[Felix Bemm]

Hi,

I have a serious problems with maker annotations especially the start 
codon placement. It started happening with maker version 2.27! About 1/3 
of my genes are missing a proper start codon. When reviewing the GFF 
files gene predictors and est evidence standalone would predict the 
right gene structure including the start codon. I was thinking that this 
problem was somehow linked to my gene models but looking at their 
standalone prediction I discarded that theory. Just some stats about 
proteins with proper start codon (first column) and missing start codon 
(second column).

Maker		9268	4215
SNAP		16577	896
Genemark	18764	290

Numbers look the same when Augustus is used (currently retraining). 
Manually using EST's in Apollo often fixes the problems but I don't want 
to check > 4000 genes for this.

Do you have any idea what could cause such a problem? If you need some 
example gff files I can send you.

Best regards
Felix

-- 
Felix Bemm
Department of Bioinformatics
University of Würzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
felix.bemm at uni-wuerzburg.de