[Bioperl-l] about the frame and strand of a blastx report

[Chris Fields]

$hsp->strand():

my $parser = Bio::SearchIO->new (-file => shift @ARGV,
                                 -format => 'blast');

while (my $result = $parser->next_result) {
    while (my $hit = $result->next_hit) {
        while (my $hsp = $hit->next_hsp) {
            print $hsp->strand,"\n";
        }
    }
}

This will give 1 or -1.

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Li Xiao
> Sent: Wednesday, May 03, 2006 1:06 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] about the frame and strand of a blastx report
> 
> Hi, anybody,
> 
>     I am working to parse a blastx report by using BioPerl modules
> (Bio::SearchIO).
> The blastx result was created by NCBI-BLAST. How i can obtain the strand (
> +
> or -)
> of query sequence against the hited protein? I tried to use the strand
> function, but
> nothing were reported. And i used the frame funtion, the result usually
> display 0,1,2,
> so, the result can not give any information about the query strand( + o r-
> ).
>   How i obtain the strand of a query squence?
> --
> *********************************************************************
> Li Xiao
> Sichuan Key Laboratory of Molecular Biology and Biotechnology
> College of Life Science, Sichuan University
> Chengdu, SiChuan, P.R.China
> TEL:86-28-85470083 FAX:86-28-85412738
> E-MAIL: nuclearn at gmail.com
> URL: http://scbi.scu.edu.cn
> **********************************************************************
> 
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