Re: DNA sequence alignment - Percent Identity
Andreas Dräger <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
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. 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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l