[Bioperl-l] BIO::SearchIO HOWTO mistake?

Anders Stegmann anst at kvl.dk
Sat Jan 14 11:50:02 EST 2006

According to the Bio::SearchIO HOWTO this, 
$hsp->seq_inds('hit', 'conserved'); 
should fetch ONLY the conserved residues in an alignment (not those
When I use: 
sub subject_seq_alignment_conserved_residues { 
my ($hsp_obj) = @_; 
my %subject_conserved_hash = (); 
my @subject_string = split , $$hsp_obj->hit_string; 
foreach ($$hsp_obj->seq_inds('hit', 'conserved')) { 
$subject_conserved_hash{$_} = $subject_string[$_ -1]; 
return %subject_conserved_hash; 
I get all residues in the alignment inclusive those that are identical! 
What's wrong? 
If the Bio::SearchIO HOWTO is wrong about this, is there an easy way to
fetch only the conserved residues? 

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