<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi </div><div>and sorry for the multiple postings. I have a list of models rescued by the <span class="Apple-style-span" style="font-family: Calibri, sans-serif; font-size: 14px; ">nonoverlaping_abinits.fasta fles (against which i blasted my missing proteins from the closely related species and further filtered out the dubious hits) and a maker gff3 file, but Carson's script gff3_select won't work, and the reason is that these abinitio models were not promoted into the maker gff3 file, thus they are not there. I refer to the gff3 file generated by gff3_merge script. Am i missing something?</span></div><div><span class="Apple-style-span" style="font-family: Calibri, sans-serif; font-size: 14px; ">Thank you, </span></div><div><span class="Apple-style-span" style="font-family: Calibri, sans-serif; font-size: 14px; ">Anastasia</span></div><div><span class="Apple-style-span" style="font-family: Calibri, sans-serif; font-size: 14px; "><br></span></div><div><br></div><div><br><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div><br><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>If you know which ab initio predictions you want to add (I.e. the ab initio promoting scenario I descibed), you can provide those predictions to the use the pred_gff option and then set keep_preds=1 and they will be maintained even without evidence. Attached is a script that would make selecting those easier. It take the MAKER generated GFF3 and a list of predictions to keep (one name per line). These might be the results of a BLAST analysis for example. It will then return the GFF3 entries for just those models selected.</div></div></blockquote></div></div></div></blockquote></div></div></div></blockquote></div><br></body></html>