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Estimation of prediction accuracy
Posted: Fri Nov 20, 2015 12:53 pm
by katharina
Originally posted in the old forum by Sammy on 01.07.2013 - 22:08
How can we estimate the accuracy of gene prediction if we are using species A parameters for prediction of species B?
Re: Estimation of prediction accuracy
Posted: Fri Nov 20, 2015 12:53 pm
by katharina
by katharina on 09.07.2013 - 15:23
First of all, in order to measure gene prediction accuracy in your target species, you need a reliable set of genes of your target species. You can construct such a gene set e.g. by using ESTs2genome or protein2genome alignments.
Then, you predicted genes in the reliable gene set using the parameter set that you like. Count how many nucleotides/exons/genes were predicted correctly as coding (TP), how many were wrongly predicted as coding (FP) and how many were wrongly not predicted as coding, i.e. overseen (FN).
Katharina
Re: Estimation of prediction accuracy
Posted: Fri Nov 20, 2015 12:53 pm
by katharina
by Sammy on 10.07.2013 - 01:34
Thanks, are you telling about
http://emboss.bioinformatics.nl/cgi-bin ... est2genome program?
Re: Estimation of prediction accuracy
Posted: Fri Nov 20, 2015 12:53 pm
by katharina
by katharina on 10.07.2013 - 14:11
I have no experience with the EMBOSS est2genome programe. We usually use PASA. But est2genome might work as well. The main point is that you need to obtain full-length gene structures in gtf format - using whatever tool.
Katharina