[BiO BB] Re: All-vs-All Global protein seq alignment score

Hongyu Zhang forward at hongyu.org
Tue Jan 11 13:01:14 EST 2005

What I usually do is a two-step method. First, I use a local alignment
programs like BLAST to quickly detect those close relatives for each
sequence; second, I use a global alignment program like ClustalW to
align those close pairs to get a global score.

If you just want to get all-vs-all Smith-Watermann alignment scores,
then you just need one step: using WU-BLAST with -postsw flag.

Hongyu Zhang
Computational biologist
Ceres Inc.

More information about the BBB mailing list