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| Hi All,
I am making a bioinformatics related program. I did BLAST in this
program and get some result.But i can not find a any module which can
give me Matching Query sequence with extra 100 bases.Here is my code -
use Bio::SearchIO;
#Blast to all sequences of Introns and mature miRNA ,store output in
file name mirna1.blast:
system("c:/downloads/bin/blastall -p blastn -i intron.txt -d
hairpin.fasta -o mirna.blast -F f");
my $in = Bio::SearchIO ->new(-format => 'blast',
-file => 'mirna.blast');
while( my $result = $in->next_result ) {
while( my $hit = $result->next_hit ) {
while( my $hsp = $hit->next_hsp ) {
my ($query_beg1, $query_end1) = $hsp->range('query');
print "(Start,End)=($query_beg1,$query_end1)\n";
#Print Matching Sequence:
my $str2 = $hsp->seq_str('match');
print "Match SEQUENCE-\n$str2\n\n";
}
}
}
I am trying to print sequence for ($query_beg1-50,$query_end1+50).
Is there any Module for it?
thanks
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