[Biojava-l] Pairwise alignment of protein sequences

[pprun]

Andreas,

How about also add the 'quality', 'Percent Identity' and 'Percent 
Similarity' values into these alignment result as the GAP does?

Thanks,
Pprun


Andreas Prlic wrote:

> 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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> 
> 
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