[Biodevelopers] Blast not symmetrical?

[Martin Heusel]

Hi Michael,

> >      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.

That's right.

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

Are the background frequencies calculated for every query/database or
are the fixed frequencies from Robinson/Robinson hardwired into the
algorithm?

For asymmetry,  only the query sequence is splitted into k-mers and
the database not, so it's possible that different HSPs can occur(?).

Bye

 Martin

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