I want to align two protein sequences. For example,
sequence 1: AYGEC
sequence 2: A(GG)C
Note that sequence 2 is always shorter than sequence 1. So gaps inevitably appear in the sequence 2 of final alignment.
My goal is to align them 1) without end-gaps and 2) no gap is allowed in (GG) of sequence 2. So the possible final alignment would be
Can anyone suggest me any available command-line tools to do it? I know many tools are allowed to set a high end-gap open penalty to prevent end gaps. But I have not found any tools to prevent gaps between assigned residues.