Why 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?

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.

Answer 1

[MathWorks Support Team]

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)