[EMBOSS] help with Profit

[Peter Rice]

Mehta, Perdeep wrote:
> Hi,
> 
> I am trying to search swissprot protein database with the "Profit"
> program. Somehow after running for a while Profit produces following out
> put that has no data in it. Here is the text in the generated output
> file.
> 
> # PROF scan using Henikoff profile pdz_henikoff.prf
> # Scores >= threshold 75 (max score 88.53)
> #
> 
> Does any one have a clue what's wrong with it?  I checked the
> installation of swissprot database it works fine I could fetch a
> sequence out with seqret.

It appears there is a problem with profiles that cover complete sequences.

When the profile (including gaps) is longer than a database sequence it 
fails to match that sequence.

We will investigate. We will also add a note to the output to say how 
many hits were found and what the maximum score was.

regards,

Peter