[Bioperl-l] Bio::Search::Tiling::MapTiling and BlastX report.

Frederic.SAPET at biogemma.com Frederic.SAPET at biogemma.com
Fri Oct 30 06:10:31 EDT 2009


I'm trying to use the new  Bio::Search::Tiling::MapTiling (I have tried 
both BioPerl 1.6.1 and the last nightly build)  module on a WuBlastX 
report after reading the documentation 
Please find in attachment the sample file I used for my test.

Here is the code I have tried :

use Bio::SearchIO;
use Bio::Search::Tiling::MapTiling;

my $blio = Bio::SearchIO->new( -format => 'blast',
                                     -file => 'WuBlastX.txt'

my $result = $blio->next_result;

while (my $hit = $result->next_hit) {
    my $tiling = Bio::Search::Tiling::MapTiling->new($hit);
    my @contextsQ = $tiling->contexts('query');
        for my $contextQ ( @contextsQ ) {
        my ($min, $max) = $tiling->range('query', $contextQ);
        my $tLengthQ = $tiling->length('query', 'exact', $contextQ);
                print "QUERY range in *$contextQ* => $min, $max 
        my @contextsS = $tiling->contexts('subject');
        for my $contextS ( @contextsS ) {
        my ($min2, $max2) = $tiling->range('subject', $contextS);
                print "SUBJECT range in *$contextS* => $min2, $max2\n";


Results printed on my terminal are :

QUERY range in *m1* => 4065, 10571 (length=7038)
QUERY range in *m0* => 7, 11037 (length=2577)
QUERY range in *m2* => 2462, 14599 (length=327)
SUBJECT range in *all* => 435, 270

I think that the right query range in m1 context should be 1170 to 10571 
(and length 6828 ?)
and subject range has to be 231 to 3563 no ?

The m1 context seems to be the best one, with 2271 amino acid aligned  (in 
4 HSP )between MySampleSeq and the Protein B9GCX0.

Could you please help me to point what is wrong ?

Thank you.

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