EMBOSS Prophecy is giving different outputs for same input file
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Entering edit mode
7.5 years ago
aravind121 ▴ 70

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

prophecy php-script emboss Gribskov • 1.3k views
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1
Entering edit mode

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

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