[Biojava-l] DNA sequence alignment - Percent Identity

Andreas Dräger andreas.draeger at uni-tuebingen.de
Tue May 18 23:49:58 UTC 2010

Hi Katerina,

> Time (ms):
> Length:
> Score:
> Query:        query,        Length:
> Target:        target,        Length:
> followed by the alignment itself.
> What is more, this result is in a String format so I have to use some string
> manipulation methods in Java to extract each value, apart from the score
> which is the value returned from the call of the pairwiseAlignment method.

I have good and bad news for you.

The bad news: So far, you are right. The current release of BioJava 
provides this information only.

But the good news: A new version has already been implemented that 
provides several get methods. With the help of these you don't even have 
to calculate the percent identity by yourself, because it is also included.

How to obtain the new implementation? Please do not use the Jar file of 
BioJava you just downloaded anymore, but anonymeously check out the 
latest code from the SVN repository. For instructions how to do that, 
please see http://biojava.org/wiki/CVS_to_SVN_Migration.

I hope this helps.


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

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

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