[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)
> #

Ah, now I see it ....

You used profit, but that only uses ungapped profiles from prophecy.
That is why it has the length limit.

With gapped alignments as input to prophecy, you need to use prophet.

A few things we could do to help:

* Check for these cases and give a warning in profit for gapped input

* Make profit and prophet use the same order of inputs (profile and 
database)

* Add a threshold to prophet to report only scores above a threshold
for alignments to a database rather than a single sequence

regards,

Peter