[Bioperl-l] print alignment from blast results file

[nisa.dar]

Hi,

I am parsing a blast results file. I have found bioperl modules to get query
string, homology string and hit string for each hit/hsp. I want to print
them in the form of an alignment instead of aligning them individually.

this is what I am doing, but it doesn't seem correct

while (my $hsp = $hit->next_hsp) {
                                        my
$start_query_num=$hsp->start('query');
					my $query_string=$hsp->query_string;
					my $end_query_num=$hsp->end('query');
					my $homology_string=$hsp->homology_string;
					my $start_hit_num=$hsp->start('hit');
					my $hit_string=$hsp->hit_string;
					my $end_hit_num=$hsp->end('hit');
					my $aln_o = $hsp->get_aln;
					$query_string=~s/\n//g;#get rid of new line characters
					$homology_string=~s/\n//g;
					$hit_string=~s/\n//g;

                         print "<h3>Alignment:</h3><br />";
			print "$start_query_num-$query_string-$end_query_num<br />";
			print "   
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;$homology_string<br />";
			print "$start_hit_num-$hit_string-$end_hit_num<br /><br />";
   
            
            
}

Please let me know how can I print them in the form of an alignment as seen
in the blast results file.

Thanks


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