can you think of any existing tool that would take a bunch of seqs in a protein fasta that ARE already ALIGNED and just merge those in a sort of a chimera-concatenate. Pieces might not overlap, and mismatches would produce X's or smth.. Like in this simple example.
>.. AAAAA---ABA------BAAAA >.. ---AAAA-------BBBAB--- >output AAAAAAA-ABA---BBBXXAAA
The need is very obvious but what I ever encounter among tools around is "concatenate only non-overlapping pieces", "restrict to the longest containing sequence", etc. The seqs are protein, and the tool need be suitable for piping, so no GUI needed. Can anyone suggest?.. Thanks in advance.