I have 2 fasta files containing the same number of sequences. I'd like to blast them pairly (seq1 in file 1 to seq1 in file 2, seq2 in file 1 to seq2 in file 2 ......) and get the highest match for each pair. For example:
>a1 ATCGATAC >b1 TAAATGTCGA ... file2.fa >a2 TGACGCTG >b2 AGCGATGA ...
I want to blast a1 to a2 and b1 to b2 ......
Is there a good way to perform this?
Thank you a lot.