[maker-devel] AED eAED QI scores??

[Carson Holt]

eAED is a little more than that.  It is still at a base pair level, but it
uses exon inference from mRNAseq and in addition has a protein evidence
overlap correction for each exon.  Sometimes the overlapping protein reading
frame doesn't perfectly match the entire model (exonerate for example can
shift the reading frames by 1 in the middle to get a better alignment and
BLAST can't).  This means that just because you have physical overlap it may
be meaningless overlap.  eAED corrects for this.  Also it can use inferred
evidence from mRNAseq.  For example if you have mRNAseq data that confirm
both ends of an exon around the splice site, but not the middle of the exon,
then there is probably enough correlated data for MAKER to confidently infer
the middle of the exon.  It then counts those base pairs as confirmed even
though they don't physically overlap.  This is common with mRNAseq data as
it can taper off in the middle of long exons or won't align correctly around
short exons.  In both cases the middle gets left out.  MAKER uses
information from the reading frame and the ab initio predictors to infer if
those regions.

Most of the time eAED and AED will be identical.  eAED can sometimes be
higher for certain mRNAseq alignments and lower for what are apparent
spurious protein alignments.

--Carson


From:  Daniel Ence <dence at genetics.utah.edu>
Date:  Friday, 21 December, 2012 12:08 PM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] AED eAED QI scores??

Hi Kapeel, the QI columns are explained in the first maker paper (Cantarel
and Yandell, Genome Research 2008).

>From pg. 189,
Table 2. Maker quality index summary

Length of the 5 UTR

Fraction of splice sites confirmed by an EST alignment

Fraction of exons that overlap an EST alignment

Fraction of exons that overlap EST or Protein alignments

Fraction of splice sites confirmed by a SNAP prediction

Fraction of exons that overlap a SNAP prediction

Number of exons in the mRNA

Length of the 3 UTR

Length of the protein sequence produced by the mRNA



eAED is the the AED edit distance at an exon level, not base pair level like
normal AED. 



Thanks,

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-bounces at yandell-lab.org
[maker-devel-bounces at yandell-lab.org] on behalf of Kapeel Chougule
[kapeelc at gmail.com]
Sent: Thursday, December 20, 2012 4:00 PM
To: maker-devel at yandell-lab.org
Subject: [maker-devel] AED eAED QI scores??

Hello, 

I ran MAKER 2.27 using the option pred_stats=1 in the control file. In the
last column of the maker output gff file I have the following annotation
quality measures.

AED:0.41 eAED:0.41 QI:0|0.5|0.4|1|1|1|5|0|278

My understanding is that with AED score 0 your annotations are in prefect
agreement with the evidence data sets and with AED 1,vice versa.

 I would like to know what is the difference between AED against eAED score.
And how do I interpret the QI cloumn?

Thank you,

-- 

Kapeel Chougule
Systems Programmer
Arizona Genomics Institute (AGI)
Thomas W. Keating Bioresearch Building
University of Arizona
1657 E. Helen Street
Tucson, AZ 85719   
www.genome.arizona.edu <http://www.genome.arizona.edu>
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