[ssml] psi-blast itteration...

[Mensur Dlakic]

Hi,

I have seen the same thing happen many times with different versions of 
BLAST and don't think it's a bug. Intuitively, I think this is because in 
the initial round the sequence is scored using the substitution matrix 
alone, while in the second iteration the profile is already built based on 
that single sequence, and naturally it comes closer to the sequence itself 
than the substitution matrix.

Cheers,

Mensur

At 10:28 AM 8/30/2003 +0100, you wrote:
>Hello everyone!
>
>Welcome to the list!
>
>I have a question regrding a psi-blast result using scop
>sunid 81250 against SPTremble ac Q8WTS6 (using a quite NR
>SPTremble as the search space).
>
>I get only a single HSP, but two itterations, and the exact
>same HSP has a better E-Value in the second itteration.
>
>Is this a bug or is there some reason why the scoring system
>can vary in this way?
>
>I am using the latest version of psiblast ca one month ago.

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| Mensur Dlakic, Ph.D.              | Tel: (406) 994-2903                |
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