[Bioperl-l] 2 psi-blast questions

Hadas Leonov hleonov at pob.huji.ac.il
Wed Jan 28 04:00:55 EST 2004

I noticed that a psi-blast report only considers new hits if the 0.0 <
E-value < 0.01 (?).
Is there any possibility to change these parameters ? especially the
0.0 limit, cause large query sequences with 60% identity might still
give an e value of 0.0, thereby causing me to miss them completely by
the standard (and comfortable) method of going through a psi blast

$result = $psi_report->round($iter);
$newHits_ref = $result->newhits;
HIT: while($hit = $result->nextSbjct) {
      	my $hitName = $hit->name;
                	$is_new =  grep  /\Q$hitName\E/, @{$newHits_ref};
		unless ($is_new )   {next HIT;}
	        #do something with the new hit


furthermore, the line : $hit = $result->nextSbjct
sometimes causes the following error message to be displayed -
-------------------- WARNING ---------------------
MSG: Possible error (2) while parsing BLAST report!
but i don't seem to find anything wrong with the actual parsing result.

any ideas?

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