I would like to ask if it is possible that I run BLAST with a list of pairs of query and reference sequence IDs?
I tried bl2seq but unfortunately it does not produce the alignment of the whole length. So, for example, if a pair of sequences can produce 4 alignments, then bl2seq will output 4 results for each alignment, each with its own percentID value, while blastall extends and joins all the alignments together, and so it produces only one value of percentID of the whole. I would like to be able to run like this blastall but for all pairs that I have selected whose ID I have put in the list. Is this possible?