[Bioperl-l] Bio::Search::HSP::GenericHSP::seq_inds

[Marc Logghe]

Hi Sendu, Chris

> > At least that is what one would expect looking at the example usage
in
> > the HOWTOs
(http://www.bioperl.org/wiki/HOWTO:SearchIO#Using_the_methods
> > second code block).
> >
> > Am I correct in believing you can only do this if your hsp query
stretch
> > starts at position 1 of the query sequence?
> 
> No...

<HOWTO>
# put all the conserved matches in query strand into an array
my @str_array = split "",$hsp->query_string;
foreach ( $hsp->seq_inds('query','conserved') ){
  push @conserved,$str_array[$_ - 1];
}
</HOWTO>

$hsp->query_string will return
'IAVEEETKTTKKNKKQ-QQQANKNKNKNKKK--TTIAPEAAIDANIAAEVHTQVL'

In my example using the 'gap' class (instead of 'conserved'), @str_array
will contain 417, 431 and 432. The off-by-one indices do not exist in
that array.
Therefore, I still think the howto shows a special case where the hsp
query sequence starts at 1 (compared to 402 in my particular example). 


> 
> 
> > Query  402  IAVEEETKTTKKNKKQ-QQQANKNKNKNKKK--TTIAPEAAIDANIAAEVHTQVL
453
> >             +A+ E   TT K +KQ ++  NK  NK  KK  T+  P+AA+ + I AE  +Q L
> > Sbjct  139  VALREALSTTFKTQKQLKENLNKQPNKQWKKSQTSTNPKAALKSKIVAEFRSQAL
193
> >
> > Now, if you call seq_inds(query => 'gap') on that particular hsp
object,
> > you get these positions: 417, 431, 432. Obviously, there is no gap
in
> > the original query sequence at these positions.
> > How do you have to read these numbers ? Remark also that for
instance
> > 417 is the res just in front of the gap.
> 
> Its purpose is to let you know the position in query or subject
> coordinates where something interesting happened in the alignment. So
> seq_inds(query => 'gap') is telling you all the places that a gap
starts
> in the alignment in terms of the query coordinates. Hence 417 etc.

So, this means you have to interpret that as a gap is coming after 417 ?

> 
> 
> (Actually, does 432 make sense? Shouldn't it be 431 twice?)
Don't know, depends on how you have to 'read' this.
Thanks for looking into this.
Regards,
Marc