Let's say I have the following toy PAIRWISE GLOBAL alignment of two sequences:
aaaa----fghijk ||||.......*** aaaabcde---iij
I wish to generate the following 'consensus' or combined sequence
The methodology is:where ever along the length of alignment, there is identity choose any one of the identical characters, when there is a gap in any one of the sequences, choose the non gap character from the other sequence, and when there is a mismatch, choose the corresponding character from the lower sequence.
The actual alignments are derived using Emboss "Needle". Are there scripts/modules available in (Bio)Perl / Python or any other tool to do this?
Thanks in advance