[Bioperl-l] Bio::Search::Tiling::MapTiling and BlastX report.
Frederic.SAPET at biogemma.com
Frederic.SAPET at biogemma.com
Fri Oct 30 10:10:31 UTC 2009
Hello
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
(http://www.bioperl.org/wiki/HOWTO:Tiling).
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, $max
(length=$tLengthQ)\n";
}
my @contextsS = $tiling->contexts('subject');
for my $contextS ( @contextsS ) {
my ($min2, $max2) = $tiling->range('subject', $contextS);
print "SUBJECT range in *$contextS* => $min2, $max2\n";
}
}
exit;
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.
Fred
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