Dear all, I have one reference plastid genome and numerous plastid genomes of other species. All mentioned genomes are annotated. I'd like to identify and extract orthologs of the genes from reference genome. The naive approach is to do so by names. Obviously, this approach is not very accurate, since annotation of some genes could be incorrect in several genomes. Moreover, very often the same genes have different names in diffrent genomes. So, i'm going to use reciprocal blast to solve my task. I see at least three possible scenario:
Make reciprocal pairwaise blast comparisons of whole reference genome vs complete sequences of all the other ones (genome vs genome).
Extract genes from reference genome and perform reciprocal pairwaise blast comparisons against complete sequences of all the other genomes (genes vs genome).
Extract genes from all genomes and make pairwaise reciprocal blast search (genes vs genes).
Which one is the most correct and straightforward? Is there a ready tool to solve tasks like mine?
Thanks!
