[Bioperl-l] bp light strand method?

[Jason Stajich]

Do you want the strand of the sbjct or the query?

$hsp->query->strand will return strand of the query
$hsp->subject->strand will return the strand of the subject (db hit)

The HSP itsself doesn't really have a strand as it is a composite object.


On Wed, 1 Aug 2001, Neil, Keith wrote:

> Hi, Im using bplight, and want to find out the strand orientation of 
> my alignment.  There doesn't seem to be a method hsp->strand ?
> And if I use the start, end methods of the subject or query, I always get
> start < end, which isn't what I want.
> 
>  Score = 34.2 bits (17), Expect = 0.012
>  Identities = 17/17 (100%)
>  Strand = Plus / Minus
>  
> Query: 1     gatcaaaaaaaaaaaaa 17
>              |||||||||||||||||
> Sbjct: 55119 gatcaaaaaaaaaaaaa 55103
>  
>  
>  Score = 34.2 bits (17), Expect = 0.012
>  Identities = 17/17 (100%)
>  Strand = Plus / Plus
>  
> Query: 1     gatcaaaaaaaaaaaaa 17
>              |||||||||||||||||
> Sbjct: 15190 gatcaaaaaaaaaaaaa 15206
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Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/