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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