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$ The University of Dundee is a registered Scottish Charity, No: SC015096 _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss