[Biojava-l] Pairwise alignment of protein sequences

[Andreas Prlic]

Hi David,

I patched the SequenceAlignent class in svn. It now displays more
scores in the produced alignment image. Also you can now request the
strings for the aligned sequences from the outside. Alignment score is
the return value from the pairwiseAlignment method....

Hope that helps...
Andreas


On Thu, Jul 9, 2009 at 11:13 AM, David Zhao<wzhao6898 at gmail.com> wrote:
> 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
>
>
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