[EMBOSS] Issues with digest

[David Martin]

We have run across some issues with digest. When trying to digest the following peptide we do not get all the expected fragments. As you can see the fragments 10-31 and 16-31 is missing as are some others.

Is this peculiar to this sequence or is there an issue in the application?

..d

$ digest asis::ACDEFGHIKLMNPQRSTVWYKKACDPRFGHI  -over -un -all -stdout
Protein proteolytic enzyme or reagent cleavage digest
Enzymes and Reagents
         1 : Trypsin
         2 : Lys-C
         3 : Arg-C
         4 : Asp-N
         5 : V8-bicarb
         6 : V8-phosph
         7 : Chymotrypsin
         8 : CNBr
Select number [1]:
Output report [stdout]:
########################################
# Program: digest
# Rundate: Tue 20 Nov 2012 10:40:26
# Commandline: digest
#    [-seqall] asis::ACDEFGHIKLMNPQRSTVWYKKACDPRFGHI
#    -overlap
#    -unfavoured
#    -allpartials
#    -stdout
# Report_format: seqtable
# Report_file: stdout
########################################

#=======================================
#
# Sequence: asis     from: 1   to: 31
# HitCount: 6
#
# Complete digestion with Trypsin yields 6 fragments
#
#=======================================

  Start     End Mol_Weight Cterm  Nterm  Sequence
      1       9   1019.133 .      L      ACDEFGHIK
     16      21    782.888 R      K      STVWYK
     10      15    757.900 K      S      LMNPQR
     23      27    560.620 K      F      ACDPR
     28      31    472.538 R      .      FGHI
     22      22    146.184 K      A      K

#---------------------------------------
#---------------------------------------
#=======================================
#
# Sequence: asis     from: 1   to: 31
# HitCount: 9
#
#
#
# Partial digest with Trypsin yields 9 extras.
# All partials shown:
#
#=======================================

  Start     End Mol_Weight Cterm  Nterm  Sequence
      1      27   3194.681 .      F      ACDEFGHIKLMNPQRSTVWYKKACDPR
      1      22   2652.072 .      A      ACDEFGHIKLMNPQRSTVWYKK
      1      21   2523.899 .      K      ACDEFGHIKLMNPQRSTVWYK
     10      27   2193.559 K      F      LMNPQRSTVWYKKACDPR
      1      15   1759.022 .      S      ACDEFGHIKLMNPQR
     10      22   1650.950 K      A      LMNPQRSTVWYKK
     10      21   1522.777 K      K      LMNPQRSTVWYK
     16      27   1453.670 R      F      STVWYKKACDPR
     16      22    911.061 R      A      STVWYKK

#---------------------------------------
#---------------------------------------
-bash-3.2$


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