MATLAB: Does CLEAVE command in the Bioinformatics Toolbox 1.1.1 (R14SP1) fail for Trypsin protease when cleavage sites are adjacent in the amino acid sequence

bioinformaticsBioinformatics Toolboxcleavepatternpeptidetrypsin

The following steps illustrate the problem:
seq='MGHQQLYWSHPRKFGQGSRSCRVCSNRHGLIRKYGLNMCRQCFRQYAKDIGFIKLD'; 
pattern='[KR][^P]';
position = 1;
cleave(seq,pattern,position)
The output of the above code is:
 ans = 'MGHQQLYWSHPR'
           'KFGQGSR'
           'SCR'
           'VCSNR'
           'HGLIR'
           'KYGLNMCR'
           'QCFR'
           'QYAK'
           'DIGFIK'
           'LD'
The peptide pattern '[KR][^P]' for Trypsin fails to cleave when cleavage sites K and R are next to each other.

Best Answer

This bug has been fixed in Release 14 Service Pack 2 (R14SP2). For previous releases, please read below for any possible workarounds:
This has been verified as an error within the documentation for Bioinformatics Toolbox 1.1.1 (R14SP1) for the CLEAVE command. The peptide pattern '[KR][^P]' for Trypsin fails to cleave when cleavage sites K and R are next to each other. The workaround is to use the '[KR](?!P)' as the peptide pattern for Trypsin protease. The example in the documentation should read as follows:
seq='MGHQQLYWSHPRKFGQGSRSCRVCSNRHGLIRKYGLNMCRQCFRQYAKDIGFIKLD'; 
pattern='[KR][^P]'; 
position=1; 
cleave(seq,pattern,position) 
pattern='[KR](?!P)'; 
cleave(seq,pattern,position)
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