Svar: Re: tblastn, retrieving no match Aa from subject string

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Svar: Re: tblastn, retrieving no match Aa from subject string

Anders Stegmann
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?

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)

Anders.


>>> Brian Osborne <[hidden email]> 27-12-05 23:52 >>>
Anders,

First, think about 3 * 349793...


Brian O.


On 12/27/05 5:15 PM, "Anders Stegmann" <[hidden email]> wrote:

> I get 349793 which I can't explain.
> what is this number telling me?





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Re: Svar: Re: 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 <[hidden email]> 27-12-05 23:52 >>>
> Anders,
>
> First, think about 3 * 349793...
>
>
> Brian O.
>
>
> On 12/27/05 5:15 PM, "Anders Stegmann" <[hidden email]> wrote:
>
>> I get 349793 which I can't explain.
>> what is this number telling me?
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12/


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