[maker-devel] Annotations from protein alignments

[Marc P. Hoeppner]

Dear list,

I have an annotation project with both protein data (it's a bird, so 
I've been using both vertebrates in general and chicken in specific), 
and huge amounts of somewhat dodgy (as in lot's of pre-mRNA) RNA-seq 
data. The chicken augustus model seems to do a decent job in seeding 
gene loci, but it's not quite perfect. I want to use protein alignments 
to create a high-confidence set of exons and subsequently a set of gene 
loci to train e.g. snap), but when testing to set protein2genome=1 I 
never get any annotations. This is also true for the test data set that 
is delivered together with Maker (hsap_). Anything I should know about 
the use of proteins to generate annotations? I left all settings in the 
config file at their defaults (except protein2genome=1). I've tried this 
with both Maker 2.30 and 2.31.

All the best,

Marc

-- 
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Marc P. Hoeppner, PhD
Group leader
BILS Genome annotation platform

Department of Medical Biochemistry and Microbiology
Uppsala University, Sweden
marc.hoepner at imbim.uu.se