[Bioperl-l] (no subject)

Andrew Stewart stewarta at nmrc.navy.mil
Fri Jan 5 17:02:51 EST 2007


After running Bio::Tools::StandAloneBlast->blastall on a collection  
of protein sequences, SearchIO then allows me to traverse the list of  
hits returned for those sequences which hits were found for.  Here's  
a question: what if I want to know which query sequences -didn't-  
produce hits?

Now, I realize I could just go back and compare the set of query  
sequences to the set of blast hits to find these 'no-hits', but I'm  
wondering if SearchIO can include the queries for which hits were not  
found.  Anyone know?  Or have any other suggestions?

Thanks,
Andrew

--
Andrew Stewart
Research Assistant, Genomics Team
Navy Medical Research Center (NMRC)
Biological Defense Research Directorate (BDRD)
BDRD Annex
12300 Washington Avenue, 2nd Floor
Rockville, MD 20852

email: stewarta at nmrc.navy.mil
phone: 301-231-6700 Ext 270




More information about the Bioperl-l mailing list