If two short sequences (A and B) come from the same gene, but I don't know the name of the gene or the organism, can I perform a BLAST (or similar) search to find the gene which has best similarity with BOTH A and B? That is, only return results where A and B align to the same full length sequence.
I realise I can do a BLAST/BLAT search for each and look for the matching entries, but I wondered if there was an automated way already in existence.