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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