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 _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
