[Biojava-l] Pairwise alignment of protein sequences

[Andreas Prlic]

Hi PPrun,

not sure about how to calculate quality, but the other scores are there now.

Andreas

On Wed, Jul 22, 2009 at 7:25 AM, pprun<pzgyuanf at gmail.com> wrote:
> 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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>
>