[maker-devel] keep_preds values

[Mikael Brandström Durling]

Hi Carson and Daniel,

That sounds more logical to me.  Then it would be appropriate to change the comment of keep_preds in the generated config files.

Would it make sense to make keep_preds a non-binary value to evaluate the concordance between ab initio models obtained from different predictors? That would assume that it is less likely to be a false positive when two or more predictors suggest the same unsported model?

Mikael


10 mar 2014 kl. 16:51 skrev Carson Holt <carsonhh at gmail.com>:

> Actually that is false. The keep_preds option is still binary.  Any value
> other than 0 sets it to true.  There was discussion about making it a
> non-binary value, but that has not been implemented.
> 
> —Carson
> 
> 
> On 3/10/14, 7:47 AM, "Daniel Ence" <dence at genetics.utah.edu> wrote:
> 
>> 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
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
>