[Bioperl-l] getting alignments out of blast reports

[Remo Sanges]

with Bio::Tools:BPlite
you can use:

my $factory=Bio::Tools::Run::StandAloneBlast->new(@params);
my $blast_report=$factory->blastall($seq);
while (my $sbjct = $blast_report->nextSbjct)	{
	while (my $hsp = $sbjct->nextHSP)	{						if (YOUR PARAMETERS)	{								print "\n".
			$hsp->querySeq."\n".
			$hsp->homologySeq."\n".
			$hsp->sbjctSeq ."\n";
			}
		}
	}


Remo Sanges
BioGeM-IGB
Naples Italy



Nandita Mullapudi wrote:

> can i use Search::IO to get alignments (i.e amino acid seqs of
> query and hit)  out of blast reports for those that fulfill given criteria
> (given e- value..etc.)? i dont see a parameter name for it in the
> documentation..
> or, i'm missing it- on a cold friday evening in georgia!
> tia,
> -nandita
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
> 
>