[maker-devel] keep_preds values

[Daniel Ence]

Hi Mikael, 

The keep_preds parameter is often used the same as a binary parameter, but it doesn't have to be. The concordance that is mentioned in the comment line is the AED for that prediction. AED is a measurement of how well a prediction is supported by the evidence and ranges from 0 - 1. A prediction with an AED of 0 matches the evidence exactly while a prediction with an AED of 1 isn't overlapped by any evidence. 

The default behavior for MAKER is to make a gene model out of a prediction with any AED <1. When you change the keep_preds option from 0 to 1, then MAKER will make a gene model out of any prediction that matches the other parameters (like single_exon, min_exon, etc). Setting the keep_preds option to somewhere in between 0 and 1 will set a ceiling on the AED required for promoting a prediction to a gene model. 

>From a user standpoint, when you will almost certainly lose gene models when you set AED at an intermediate value, but you might benefit by knowing that all your models will now have an AED of at least a certain value. 

I hope that helps; let me know if it didn't. 

~Daniel

PS The original paper that described the AED is Eilbeck et al in BMC Bioinformatics 2009. It's also discussed in more detail in the MAKER2 paper, the MAKER-P paper, and the Yandell and Ence Nature Reviews Genetics paper from 2012. 

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 [maker-devel-bounces at yandell-lab.org] on behalf of Mikael Brandström Durling [mikael.durling at slu.se]
Sent: Monday, March 10, 2014 4:27 AM
To: maker-devel at yandell-lab.org
Subject: [maker-devel] keep_preds values

Hi,

Can someone, please, explain the keep_preds parameter, as it works now with a value between 1 and 0? It used to be binary, but now it seems to test concordance towards something. The maker wiki doesn’t explain it any further either.

Thanks,
Mikael


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