[maker-devel] Expected format for EST GFF3

[Carson Holt]

Match/match_part features are expected.  MAKER expects these to be polished
(I.e. correctly aligned around splice sites).  For example exonerate, BLAT,
and cufflinks results will be correct around splice sites and can be used;
BLAST results on the other hand will not be correct and should not be used.

The Gap attribute is used by maker if available, but is not required (Gap
describes how to reconstruct an alignment for gaps and mismatches).
Otherwise MAKER assumes all positions are matches to the reference.

Thanks,
Carson


From:  Daniel Standage <daniel.standage at gmail.com>
Date:  Thursday, 4 October, 2012 2:52 PM
To:  Maker Mailing List <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Expected format for EST GFF3

Greetings.

I would like to use Maker's est_gff option to include EST evidence from an
external GFF3 file. In addition to being a valid, well-formed GFF3 file,
what expectations does Maker assume about the contents of this file? Which
feature types are expected and/or supported? Thanks!

--
Daniel S. Standage
Ph.D. Candidate
Bioinformatics and Computational Biology Program
Department of Genetics, Development, and Cell Biology
Iowa State University

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