Hi, I used glimmer to prediction orfs in a draft genome, and I found that some orf had a insertion or deletion with its homologous genes in other genomes. But I used these homologous genes to search the draft genome sequence and got a complete match with total length. So, the predicted orf is wrong? or the predicted needs to be tuned again. how to get a credible gene prediction results? Thank you for your reply.
This is a well understood problem with using ORF finders like glimmer (and pretty much anything else) on data that is likely to have insertion/deletion (frameshift) errors. When FASTX was published in 1997 (Pearson et al, (1997) Genomics 46:24-36), we showed that there were many genes in a recently sequenced bacterial genome that could be extended by alignment with frameshifts.
I would argue that there is no reason to look for open reading frames. FASTX (and BLASTX, but you need to turn on the option that allows frame-shifts) will find all the genes you can find with ORF-finders, and more (because they are not limited to a minimum ORF length).