Re: Blast not symmetrical?

Hello, Martin!

I am looking for the spot in the algorithm that is the reason for the
asymmetry in blast.

I'm not sure if I got your argument but

> > Where does the background distribution of the amino acid (or in my case
DNA)
> > sequence of the query come in?
>
>      Spw_ij =  log( Q_ij / (P(i) P(j) )) / λ

this is used for the construction of a scoring matrix. The frequencies here
are not taken from the actual blast search.

This is the formula with which lambda is estimated:

> For λ the equation
>
>  sum_i,j P(i) P(j) exp(λSij) = 1
>
> must hold.
>

This would give rise to asymmetry if P(i) and P(j) are only calculated from
the database sequence and the query is ignored.

Is this the case?

Regards,
Michael.