[maker-devel] MAKER prediction- evidence weightage

[Carson Holt]

Not so much "weight" as much as different evidence types help infer
different parts of a gene model.  ESTs can be used to infer introns, UTR,
and splice sites.  Proteins help infer exons and CDS.  They become "hints"
to the gene predictors for the location of these sub-features.  Then if ESTs
have matching exons that extend beyond the new model produced by SNAP or
Augustus using the hints, then they can be added on directly as UTR.

That error can happen in the older version 2.10, but should not happen with
2.27.  To get rid of it you have to edit several lines of code in maker and
BioPerl to remove every mention of SDBM_File.  It really doesn't effect
anything, as the module in question ends up using DB_File regardless.

Thanks,
Carson



From:  Sivaranjani Namasivayam <ranjani at uga.edu>
Date:  Tuesday, 26 February, 2013 11:22 PM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] MAKER prediction- evidence weightage

Hi,

Does MAKER give more weightage to certain type of evidence than others, that
is, does it base its annotation more on EST, protein or ab-initio gene
prediction? If so which one and is there a way to alter this.

Also, when I run MAKER I see the following in the error/log file

Can't locate package SDBM_File for @AnyDBM_File::ISA at
/usr/local/perl/5.14.1/l
ib/5.14.1/x86_64-linux-thread-multi/DB_File.pm line 293.

Can you please tell me how this impacts the results.

Thanks,
Ranjani
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