[Bioperl-l] tblastn, retrieving no match Aa from subject string

Anders Stegmann anst at kvl.dk
Tue Dec 27 17:15:52 EST 2005


I am blasting a protein seq against a chromosome by using tblastn in a bioperl script.

my protein seq is 1250 Aa corresponding to 3750 nt.
by doing:

 $hsp->start('hit')     I get 1045637
 $hsp->end('hit')       I get 1049386

which is okay.

by doing: 

 foreach ($hsp_obj->seq_inds('query', 'nomatch')) {

		print $_, "\n";


I get 2, which okay because I made a Aa substitution in the query seq at position two.

but when I go:

 foreach ($hsp_obj->seq_inds('hit', 'nomatch')) {

		print $_, "\n";


I get 349793 which I can't explain.
what is this number telling me?
According to the Bio::SearchIO HOWTO I should get the position of the not matching Aa the subject DNA seq. I guess that because I am using tblastn I get the position of a nucleotide in the codon of the not matching Aa, but that doesn't correspond to start and end positions written above.

The easiest way out of this would be if I somehow could retrieve the not matching Aa position from the translated protein hit string. As I can when two proteins are blasted agsinst each other.
does anybody know how? 
(note: as the script works when two proteins are blasted against each other the code should be okay)

Regards Anders.

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