Bioinformatics Toolbox™

cleave - Cleave amino acid sequence with enzyme

Syntax

Fragments = cleave(SeqAA, PeptidePattern, Position) [Fragments, CuttingSites] = cleave(...) [Fragments, CuttingSites, Lengths] = cleave(...) cleave(..., 'PropertyName', PropertyValue,...) cleave(..., 'PartialDigest', PartialDigestValue)

Arguments

`SeqAA`	Amino acid sequence. Enter a character string or a vector of integers from the table Mapping Amino Acid Letter Codes to Integers. 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`.
`PartialDigestValue`	Property to specify the probability that a cleavage site will be cleaved. Enter a value from `0` to `1` (default).

Description

Fragments = cleave(SeqAA, PeptidePattern, Position) cuts an amino acid sequence (SeqAA) into parts at the specified cleavage site specified by a peptide pattern and position.

[Fragments, CuttingSites] = cleave(...) returns a numeric vector with the indices representing the cleave sites. A 0 (zero) is added to the list, so numel(Fragments)==numel(CuttingSites). You can use CuttingSites + 1 to point to the first amino acid of every fragment respective to the original sequence.

[Fragments, CuttingSites, Lengths] = cleave(...) returns a numeric vector with the lengths of every fragment.

cleave(..., 'PropertyName', PropertyValue,...) defines optional properties using property name/value pairs.

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`

Examples

Get a protein sequence from the GenPept database.
```
S = getgenpept('AAA59174')
```

Cleave the sequence using trypsin. Trypsin cleaves after K or R when the next residue is not P.

[parts, sites, lengths] = cleave(S.Sequence,'[KR](?!P)',1);
    for i=1:10
        fprintf('%5d%5d   %s\n',sites(i),lengths(i),parts{i})
    end

  0    6   MGTGGR
  6    1   R
  7   34   GAAAAPLLVAVAALLLGAAGHLYPGEVCPGMDIR
 41    5   NNLTR
 46   21   LHELENCSVIEGHLQILLMFK
 67    7   TRPEDFR
 74    6   DLSFPK
 80   12   LIMITDYLLLFR
 92    8   VYGLESLK
100   10   DLFPNLTVIR

cleave - Cleave amino acid sequence with enzyme

Syntax

Arguments

Description

Examples

See Also