[Bioperl-l] bioperl BLAST question

Sean ohEigeartaigh s_oheigeartaigh at yahoo.co.uk
Mon Jul 6 15:01:04 UTC 2009


I'm trying to use bioperl to limit the number of BLAST results. However, when I use the following bit of code, it limits to less than the cutoff number, and excludes BLAST results that are halfway up the BLAST results page (without the limit) which it shouldn't exclude.

$blast = Bio::Tools::Run::StandAloneBlast
    ->new(program => 'tblastn', database =>$blastdb, b =>100, v =>100, F=>$fil, outfile=>$out)

Using this bit of code, I get 60 results for my query (out of 173 with no hit limit and an e-value cutoff of e=10). If I use b =>150, v=>150, I get 85 results, and some BLAST results appear halfway up the results page. In other words, the limit seems to be removing results at random throughout the file, and is also not giving me enough results.

Am I using the b and v parameters (to limit blast results and blast one-line summaries) incorrectly?

Thanks very much for your help,
Seán Ó hÉigeartaigh


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