| Bioinformatics Toolbox | |
Cleave amino acid sequence with enzyme
cleave(SeqAA, PeptidePattern, Position, 'PropertyName', PropertyValue...) cleave(... 'PartialDigest', PartialDigestValue)
SeqAA | Amino acid sequence. Enter a character string or a vector of integers from the table . Examples: 'ARN' or [1 2 3]. You can also enter a structure with the field Sequence. |
PeptidePattern | Short amino acid sequence to search in a larger sequence. Enter a character string, vector of integers, or a regular expression. |
Position | Position on the PeptidePattern where the sequence is cleaved. Enter a position within the PeptidePattern. Position 0 corresponds to the N terminal end of the PepetidePattern. |
| PartialDigest | Property to set the probability that a cleavage site will be cleaved. Enter a value from 0 to 1. The default value is 1. |
cleave(SeqAA, PeptidePattern, Position) cuts an amino acid sequence (SeqAA) into parts at the specified cleavage site specified by a peptide pattern and position.
cleave(... 'PartialDigest', PartialDigestValue) simulates a partial digestion where PartialDigest is the probability of a cleavage site being cut.
The following table lists some common proteases and their cleavage sites.
Protease | Peptide Pattern | Position |
Trypsin | [KR][^P] | 1 |
Chymotrypsin | [WYF][^P] | 1 |
Glutamine C | [ED][^P] | 1 |
Lysine C | [K][^P] | 1 |
| Aspartic acid N | D | 1 |
S = getgenpept('AAA59174')
% Trypsin cleaves after K or R when the next residue is not P
parts = cleave(S.Sequence,'[KR][^P]',1);
Bioinformatics Toolbox functions restrict, seqshowwords
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