[maker-devel] est2genome=1 for est and altest

[Daniel Ence]

Hi Marc, This is a partial answer to your question. I don't know the full reason that models aren't built from altest evidence, but I do know that those sequences are aligned with tblastx (nucleotide translated to protein and back to nucleotide) and not with blastn with relaxed parameters. 

Also the final protein and nucleotide alignments that do get made into models are made by exonerate and not by blast. 

Does that help?

~Daniel


Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
________________________________________
From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of Marc Höppner [mphoeppner at gmail.com]
Sent: Monday, September 01, 2014 7:07 AM
To: maker-devel at yandell-lab.org
Subject: [maker-devel] est2genome=1 for est and altest

Hi,

I may be wrong about this, but it seems to me that Maker will never build a gene model from EST evidence, if the set data is provided as ‘altest' rather than ‘est'. In my case, I am annotating a plant for which there is a closely related reference genome + annotation, as well as pretty good EST data. So I supplied the EST data as ‘altest', assuming that the only difference would be that the alignment parameters would be slightly more relaxed. But I found that Maker never made any genome models from that data. When moving the EST data to ‘est’, it worked.

So I am not sure whether this is an intended behaviour, but in my case it caught me a bit by surprise…

Regards,

Marc
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