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

[Jason Stajich]

On Dec 28, 2005, at 1:08 PM, Anders Stegmann wrote:

> Thanks again, it helped!
>
> I have two related questions:
>
> 1) how can I tell if my translated protein is a reverse complement  
> derived from a gene on the opposite chromosome strand?
>
$hsp->hit->strand  or $hsp->strand('hit)
> 2) why do I get the position and type of the substituted Aa when I  
> blast the protein against its own gene seq, when I only get a  
> position when it is blasted against a chromosome seq? (just out of  
> curiousity)
>
I don't understand what you mean at all, concrete data example would  
be more helpful.
> Anders.
>
>
>>>> Brian Osborne <osborne1 at optonline.net> 27-12-05 23:52 >>>
> Anders,
>
> First, think about 3 * 349793...
>
>
> Brian O.
>
>
> On 12/27/05 5:15 PM, "Anders Stegmann" <anst at kvl.dk> wrote:
>
>> I get 349793 which I can't explain.
>> what is this number telling me?
>
>
>
>
>
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12/