[ssml] Problem with MAST searches

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Sat Dec 2 13:19:06 EST 2006

Gregor Warsow wrote:
> If we search with 1 motif (PSSM, position-specific scoring matrix),
> MAST lists e.g. 10 hits of that single motif. If we
> do the search with 2 motifs by adding a second PSSM to the first one, we get a
> much longer list of results. Surprisingly, there are more than those 10 hits
> that feature _only_ motif 1 from the first query.
> We have no explanation for this surpising behaviour.
> Do you have any idea? How can we make sure to receive all matching subsequences,
> including the ones we get if we search with a second motif,
> when searching with only one PSSM?

Hey Gregor,

Interesting problem! Can you send as much detail as you can about the 
searches you are performing? What happens if you only search the second 
motif? (i.e. do you loose hits in a similar fashion?)

One possibility that springs to mind is that the two motifs together 
have better e-values than the one motif alone, which would mean that the 
hits to the first motif get filtered out by the default e-value filter. 
Only when the two occur together is the hit significant, resulting in 
more hits to the first motif when you search both.

Not too familiar with mast, so I don't know if this is a plausible 
explanation. Can you try different e-value cutoffs and see if this makes 



> Any help would be very much appreciated.
> Gregor Warsow
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