[Biojava-l] Pairwise alignment of protein sequences

[David Zhao]

David Zhao <wzhao6898 <at> gmail.com> writes:
I found the answer from a post here(http://portal.open-
bio.org/pipermail/biojava-l/2007-February.txt#). In short, I need to use 
AlphabetManager.alphabetForName("PROTEIN-TERM"); instead of 
AlphabetManager.alphabetForName("PROTEIN"); to parse the matrix file.
Another question though, now I have the alignment, 
how do I retrieve score and 
mismatch, gap information from it?
 Time (ms):	62
 Length:	25
  Score:	180
  Query:	query,	Length:	25
  Target:	target,	Length:	25


Query:	  1 KLFVGGIKEDTEEHHLRDYFEEYGK 25 
            | ||||||||||||||||||| ||| 
Target:	  1 KIFVGGIKEDTEEHHLRDYFEQYGK 25 

Thanks!

David