[ssml] psi-blast itteration...

[Dan Bolser]

Mensur Dlakic said:
> 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.


Would the difference in e value be more prounounced in the second itteration
if the first HSP had a low e value?

What additional information over the substitution matrix is used in the second
itteration when we only use a single sequence in the profile?

Does it work like this...

1 take query, make profile
2 query
3 get hsps, rebuild profile
4 query

Is this a reason for including query sequences in the search space? (to track
the value of self hits)?

Thanks




> 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.
>
> ========================================================================== |
> Mensur Dlakic, Ph.D.              | Tel: (406) 994-2903                | |
> Department of Microbiology        | Fax: (406) 994-4926                | | Montana
> State University          | http://www.umich.edu/~mensur/      | | 109 Lewis Hall,
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>           | E-mail: mdlakic at montana.edu        |
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