[Bioperl-l] parsing blast reports- co-ordinate of hit

[Marc Logghe]

Hi Nandita,

> -----Original Message-----
> From: Nandita Mullapudi [mailto:nandita at uga.edu]
> Sent: donderdag 29 april 2004 23:01
> To: bioperl-l at portal.open-bio.org
> Subject: [Bioperl-l] parsing blast reports- co-ordinate of hit
> 
> 
> Hi all,
> I need to extract from zillion blast reports the numerical 
> co-ordinates of the query as well as the hit. Am using Bio::SearchIO 
> and $hsp->start  and $hsp->end get me the co-ordinates of the query, 
> but how do i get the corresponding co-ordinates of the hit?

You only have to pass the arguments 'query' or 'hit', e.g. in your case
$hsp->start('hit')
See also http://bioperl.org/HOWTOs/html/SearchIO.html table1  (SearchIO methods)

Regards,
Marc