[Biojava-l] Pairwise alignment of protein sequences

[pprun]

Great!

Just saw the new add-in after using the latest code in Trunk.

Cheers
Pprun


Andreas Prlic wrote:

> 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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>>
>>
> 
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