(I am defining ORF as, between an ATG start and a downstream stop codon)
Given a situation like this:
showing a ~1kb region, forward strand, 3 frame prediction of starts (green) and stops (red), for the frame 3 span between the first and second stops, the ORF finding tools I've tried all return a single long ORF. But I need to list all the possible frame 3 ORFs in that span, i.e., the ORFs that start from different ATGs but all end with the same stop. So my desired tool would would would actually report 10 ORFs for the span in question. Is there any tool that outputs this?
I have tried ORF finder (NCBI) and getorf (emboss) and orfipy . There are no setting I can find in any of those, so far, that can do what I want.