[Biojava-l] getting % identity from blast search results

Susan Glass SGlass@wyeth.com
Thu, 06 Jun 2002 18:45:43 -0400

Hello there,
     Last year I wrote a class that parsed a BLAST search file and returned a List of SequenceDBSearchResults, using BlastLikeSAXParser and BlastLikeSearchBuilder.  I modelled it on demo code that David Waring had written (thanks!).  Once the results were returned, I picked the hits that were below a given evalue cutoff.
    My problem now is that the client has requested that instead of an evalue cutoff, the program should pick all hits that match, say, with 90% identity over 90% of the query sequence length.  I'm not sure how to get the identity information, since SequenceDBSeachHit and SequenceDBSearchSubHit don't have fields for this info.  In browsing through the demos it seems that blast2html has a handler that creates its own classes (HSP, HSPSummary) that accesses this info, which might be a good starting point for new code. 
     I was wondering if anyone else has already encountered this problem, and could possibly point me in the right direction.  Any help would be appreciated.