org.expasy.mzjava.proteomics.mol.digest

Class CleavageSiteMatcher

java.lang.Object

org.expasy.mzjava.proteomics.mol.digest.CleavageSiteMatcher

public class CleavageSiteMatcher
extends Object

This matcher is used to find the sites of cleavage in an amino-acid sequence. The CleavageSiteMatcher is constructed from a string that represents the cleavage pattern. The pattern is based on regex except that the | indicates the cleavage site instead of an or. The pattern consists of the amino acids that are matched to the left of the cut followed by | and then the amino acids matched to the right of the cut. K|X specifies that the cut is after every K (X is any amino acid). Amino acids that should not match can be specified using ^. K|[^P] specifies that the cut should be after every K except is it is followed by a P. As with regex any character class can be used to specify a position not just negation. [KR]|[^P] specifies that the cut should be after every K or R except if followed by P. The pattern can be extended to more than one amino acid either side of the clevage site. For example [^P][FL]X[FLY]|[^P]X[^K] is a valid pattern that checks 4 amino acids to the left and three amino acids to the right of the cleavage site. For Proteases that have two distinct patterns an "or" can be used. To cut before and after K "K|X or X|K" can be used. The formal definition of the pattern defining the site is:

Formal definition of a cleavage site

• Site_altern := Site (or Site)*
• Site := Symbol_aa+ Cut-token Symbol_aa+
• Symbol_aa := AA | AA_class | TERM_class
• TERM_class := 'ont{'(AA | AA_class)+'}' | 'oct{'(AA | AA_class)+'}'
• AA := Symbol_aa_namb | Symbol_aa_amb
• Symbol_aa_namb := [AC-IK-TVWY]
• Symbol_aa_amb := [BJUXZ]
• AA_class := '[' AA ']'
• Cut-token := '|'

Examples:

[KR]|[^P] is the pattern for trypsin (cut after K or R except if followed by P) DEVD|X or R|K this cuts to the right of DEVD or between R and K DEBD|X[^P]

To control the matching at the beginning or end of the protein the ont{} and oct{} (or N term & or C term) can be used to match the term or the pattern in the brackets for example:

ont{[^P]}X|S cuts ASPASS into A SPAS S

http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html

Author:

nikitin, Oliver Horlacher

Constructor Summary

Constructors

Constructor and Description
CleavageSiteMatcher(String cleavageFormat) Pattern has a special format: Pn ...
CleavageSiteMatcher(String cleavageFormat, com.google.common.base.Optional<Modification> nTermMod, com.google.common.base.Optional<Modification> cTermMod)

Method Summary

Methods

Modifier and Type	Method and Description
com.google.common.base.Optional<Modification>	getCtermMod()
String	getFormat()
com.google.common.base.Optional<Modification>	getNtermMod()
Pattern	getRegex()
boolean	hasCtermMod()
boolean	hasNtermMod()
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

CleavageSiteMatcher

public CleavageSiteMatcher(String cleavageFormat)
                    throws CleavageSiteParseException

Pattern has a special format:

Pn ... P4 P3 P2 P1 | P1' P2' P3' ... Pm'

Throws:

CleavageSiteParseException - if s is not a valid string

CleavageSiteMatcher

public CleavageSiteMatcher(String cleavageFormat,
                   com.google.common.base.Optional<Modification> nTermMod,
                   com.google.common.base.Optional<Modification> cTermMod)
                    throws CleavageSiteParseException

Parameters:

cleavageFormat - the cleavage site

nTermMod - protease may modify peptide digest at nterm

cTermMod - protease may modify peptide digest at Cterm

Throws:

CleavageSiteParseException - if s is not a valid string

Method Detail

getFormat

public String getFormat()

getRegex

public Pattern getRegex()

getNtermMod

public com.google.common.base.Optional<Modification> getNtermMod()

Returns:

the Nt modification.

getCtermMod

public com.google.common.base.Optional<Modification> getCtermMod()

Returns:

the Ct modification.

hasNtermMod

public final boolean hasNtermMod()

Returns:

true if add Nt modification.

hasCtermMod

public final boolean hasCtermMod()

Returns:

true if has Ct modification.

toString

public String toString()

Overrides:

toString in class Object