[maker-devel] Precomputed alignments

[Carson Holt]

With the Target and Gap attribute you get slightly better behavior on
filtering when you specify the blast_depth=X parameter in the
maker_bopts.ctl file (keeps only X best hits).  They will also affect the
eAED score since it takes reading frame into account (so no Gap attribute
means no assumption of reading frame).  Otherwise they are only beneficial
for seeing the alignment in a viewer as some viewers can recover the
alignment when those values are specified.  If you are not using blast_depth
or trying to view the alignments in a viewer they don't really do anything.
MAKER will just assume perfect match across the specified regions.

--Carson



From:  Daniel Standage <daniel.standage at gmail.com>
Date:  Saturday, May 31, 2014 at 9:23 AM
To:  Maker Mailing List <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Precomputed alignments

Hello again!

About a year ago I asked about using precomputed alignments with Maker. The
thread quickly took a different direction as we tried to track down other
issues, and I never got the thread back on its original track.

So, to return to the original question, what exactly is required when
providing pre-computed alignments in GFF3 format? For example, does it
affect Maker's behavior whether a score is given? The "Target" attribute?
The "Gap" attribute?

Thanks!

--
Daniel S. Standage
Ph.D. Candidate
Computational Genome Science Laboratory
Indiana University
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