EMBOSS Prophecy is giving different outputs for same input file

Question

[aravind121]

I have written a small php script(long back) for calculating gribskov score using prophecy.

/usr/local/bin/EMBOSS-6.5.7/emboss/prophecy $domfile.aln -type G -datafile Epprofile -name TEST -threshold 75 -open 3 -extension 0.3 -outfile $domfile.prophecy

I was running the same script with same input file, but I am getting diifent output. I have not changed anything else in the script.

Old Out_Put:

  # Last column is indel penalty
  # Rows are alignment positions 1->n
  Gribskov
  Name            TEST
  Matrix          pprofile
  Length          136
  Max_score       588.31
  Threshold       75
  Gap_open        3.00
  Gap_extend      0.30
  Consensus       MAAIRPLYKPKIVKKRTKKFIRHQSDRYVKLKNRNWRKPKGIDNRVRRRFKGQYLMPNIGYGSNKKTRHMLPNGFKKFLVHNVKELEVLMMQNRKYCAEIAHNVSSKKRKAIVERAAQLSIRVTNPNARLRSEENE

New Out_Put

# Last column is indel penalty
  # Rows are alignment positions 1->n
  Gribskov
  Name            TEST
  Matrix          pprofile
  Length          136
  Max_score       1715.52
  Threshold       75
  Gap_open        3.00
  Gap_extend      0.30
  Consensus       MAAIRPLYKPKIVKKRTKKFIRHQSDRYVKLKNRNWRKPKGIDNRVRRRFKGQYLMPNIGYGSNKKTRHMLPNGFKKFLVHNVKELEVLMMQNRKYCAEIAHNVSSKKRKAIVERAAQLSIRVTNPNARLRSEENE

You can notice change in Max-Score of both the outputs, I have not included profiles for readability. Even they look completely different. Why I am getting this type of difference with same script and input. ?

Thanks in advance

[Istvan Albert]

well, the simplest and mostly likely answer is that you might have not invoked the program the same way, or that the program has been updated in the meantime