[maker-devel] AED eAED QI scores??

[Daniel Ence]

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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