Fast Optimal Global Sequence Alignment Algorithm
Switch branches/tags
Clone or download
Pull request Compare This branch is even with kjenova:master.
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Type Name Latest commit message Commit time
Failed to load latest commit information.


== NOTES ==
Having an alignment matrix is obsolete. The code for dealing with the worst case problem (which would almost never happen in biological data), i.e. when the the other sequence has nothing in common with the first, is hidden in print_alignment()—notice, that there is no "elseif alignments[x, y] == XY" but an "else", so the two alignment string in the worst case are the strings themselves + neccesarry gaps, so the initial alignment should be just that. We should propose a new alignment string (one gapped string for each sequence) in the main loop, and update that if it is better.