Good afternoon,
I am carrying out some gene predictions on my species of interest, using the AUGUSTUS parameters defined by training on WebAUGUSTUS.
By performing gene prediction with the utr=on option, the number of genes predicted is significantly reduced compared to the gene prediction with the utr=off option. In addition, when the UTR option is on, all predicted genes start at nucleotide 1 of the scaffolds into which the genome of interest is divided. I wanted to try to understand a possible explanation to these results.
Thank you very much, best regards,
Simone
Gene prediction with UTR=on option
Moderator: bioinf
Re: Gene prediction with UTR=on option
Fully automated UTR training of AUGUSTUS sometimes works great, and sometimes produces really poor results, as in your case. To date, I have no automated way to "know" beforehand.
In some cases, the problem can be improved upon by setting the /UtrModel/polyasig_consensus in ${species}_parameters.cfg . You can also play with the pattern weight parameters in the same file.
In some cases, the problem can be improved upon by setting the /UtrModel/polyasig_consensus in ${species}_parameters.cfg . You can also play with the pattern weight parameters in the same file.