To perform sequences similarity search, we usually use NCBI BLAST. However, we often need to parse the result to split the sequences which have significant and/or insignificant hits, respectively. Here is the sample to do this work via bioperl, I hope it will supply useful information to you. Thank you!
#!/usr/bin/perl -w
use strict;
use Bio::SearchIO;
my $query = "";
my $SeqId = undef;
my %hit = ();
my %Seq = ();
my %Des = ();
open (PNI, "seq.fasta");
while (my $line =
) {
if ($line =~ /^>(\S+)\s*.*$/) {
$SeqId = $1;
$Des{$SeqId} = $line;
} else {
$Seq{$SeqId} .= $line;
}
}
close PNI;
open (NO, ">nohits.fasta");
open (HIT, ">hits.fasta");
my $in = new Bio::SearchIO(
-format => 'blast',
-file => 'blast.txt');
while(my $result = $in->next_result) {
$query = $result->query_name;
while (my $hit = $result->next_hit) {
$hit{$query} = $hit->name;
}
if (!defined $hit{$query}) {
#$hit{$query} = "No hits found";
print NO $Des{$query};
print NO $Seq{$query};
} else {
print HIT $Des{$query};
print HIT $Seq{$query};
}
}
close NO;
close HIT;
