[ssml] psi-blast itteration...

[Dan Bolser]

Mensur Dlakic said:
> Disclaimer: I am no BLAST expert, so some of the things I say below are  just
> common(ly wrong) sense.
>
>>Would the difference in e value be more prounounced in the second itteration if
>> the first HSP had a low e value?
>
> I think so. I routinely set E-value lower than h-value for PSI-BLAST  iterations
> and often see that E-values improve quite a lot for many  sequences, though not
> necessarily below the h-value so they don't get  included in the profile.

I can see why this would happen, and why you would want it to happen,
But I think that for a single sequence hit the second itteration e-value
may misrepresent the actual significance - I guess this is the problem with
profile itteration and false +ve hits!

>>Is this a reason for including query sequences in the search space? (to track the
>> value of self hits)?
>
> I think that it has to be included, if for no other reason than only to  have
> something for alignments. That said, I have seen that with some  profiles the
> query sequence will stop being the best match after a few  iterations, meaning
> that it'll move down the list a bit.

Has this drift been studied in detail?

Any refs?

Cheers,
Dan.