[Biojava-l] Pairwise alignment of protein sequences

[Andreas Dräger]

Hi guys,
> not sure about how to calculate quality, but the other scores are there now.
>   
>> How about also add the 'quality', 'Percent Identity' and 'Percent
>> Similarity' values into these alignment result as the GAP does
>>     
Yes, calculating "quality" or "similarity" is a bit unclear. The score
is actually the measurement for similarity and therefore also kind of
quality. What can be done is to add a feature for the percent identity.
However, we have to distinguish between two different things: An
alphabet may contain matching symbols, i.e., symbols that are considered
equivalent, and identical symbols. This fact makes it a bit harder to
calculate the identity because there is the question if we should
consider matching symbols identical.

Cheers,
Andreas

-- 
Dipl.-Bioinform. Andreas Dräger
Eberhard Karls University Tübingen
Center for Bioinformatics (ZBIT)
Sand 1
72076 Tübingen
Germany

Phone: +49-7071-29-70436
Fax:   +49-7071-29-5091