org.biojava.bio.molbio

Class RestrictionEnzyme

java.lang.Object

org.biojava.bio.molbio.RestrictionEnzyme

All Implemented Interfaces:

Serializable

public class RestrictionEnzyme
extends Object
implements Serializable

RestrictionEnzyme represents a restriction enzyme according to the REBASE standard. The cut positions are indicated relative to the 5' end of the recognition site and occur downstream of the given residue. Note that some enzymes cut in more than one position and that cut positions may occur outside the recognition site.

Since:

1.3

Author:

Keith James, George Waldon

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	BLUNT BLUNT the end type created by enzymes which leave a blunt end.
static int	CUT_COMPOUND CUT_COMPOUND a cut type where the enzyme cuts in two positions relative to the recognition site.
static int	CUT_SIMPLE CUT_SIMPLE a cut type where the enzyme cuts in one position relative to the recognition site.
protected int	cutType
protected int[]	dsCutPositions
protected String	forwardRegex
protected String	name
static int	OVERHANG_3PRIME OVERHANG_3PRIME the sticky end type created by enzymes which leave a 3' overhang (e.g. a stretch of single-stranded DNA with a free 3' end).
static int	OVERHANG_5PRIME OVERHANG_5PRIME the sticky end type created by enzymes which leave a 5' overhang (e.g. a stretch of single-stranded DNA with a free 5' end).
protected String	reverseRegex
protected SymbolList	site
protected int[]	usCutPositions

Constructor Summary

Constructors

Constructor and Description
RestrictionEnzyme(String name, SymbolList site, int dsForward, int dsReverse) Creates a new RestrictionEnzyme which cuts within or downstream of the recognition site.
RestrictionEnzyme(String name, SymbolList site, int usForward, int usReverse, int dsForward, int dsReverse) Creates a new RestrictionEnzyme of the unusual type which cuts both upstream and downstream of its recognition site.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object o)
double	getCuttingSize() The cutting size of a restriction enzyme is defined has the number of nucleotides that are directly involved in the recognition sequence.
int	getCutType() getCutType returns the type of cut produced by the enzyme.
int[]	getDownstreamCut() getDownstreamCut returns the cut site within or downstream of the recognition site.
int	getDownstreamEndType() getDownstreamEndType returns the double-stranded end type produced by the primary (intra-site or downstream) cut.
String	getForwardRegex() getForwardRegex returns a regular expression which matches the forward strand of the recognition site.
String	getName() getName returns the enzyme name.
RestrictionEnzyme	getPrototype() The prototype is a RestrictionEnzyme that represents a set of isoshizomers.
SymbolList	getRecognitionSite() getRecognitionSite returns the forward strand of the recognition site.
String	getReverseRegex() getReverseRegex returns a regular expression which matches the reverse strand of the recognition site.
int[]	getUpstreamCut() getUpstreamCut returns the cut site upstream of the recognition site.
int	getUpstreamEndType() getUpstreamEndType returns the double-stranded end type produced by the secondary (upstream) cut.
int	hashCode()
boolean	isPalindromic() isPalindromic returns true if the recognition site is palindromic.
boolean	isPrototype()
void	setProtype(RestrictionEnzyme proto) Set the prototype of this RestrictionEnzyme.
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

CUT_SIMPLE

public static final int CUT_SIMPLE

CUT_SIMPLE a cut type where the enzyme cuts in one position relative to the recognition site. This covers the vast majority of cases.

See Also:

Constant Field Values

CUT_COMPOUND

public static final int CUT_COMPOUND

CUT_COMPOUND a cut type where the enzyme cuts in two positions relative to the recognition site.

See Also:

Constant Field Values

OVERHANG_5PRIME

public static final int OVERHANG_5PRIME

OVERHANG_5PRIME the sticky end type created by enzymes which leave a 5' overhang (e.g. a stretch of single-stranded DNA with a free 5' end).

See Also:

Constant Field Values

OVERHANG_3PRIME

public static final int OVERHANG_3PRIME

OVERHANG_3PRIME the sticky end type created by enzymes which leave a 3' overhang (e.g. a stretch of single-stranded DNA with a free 3' end).

See Also:

Constant Field Values

BLUNT

public static final int BLUNT

BLUNT the end type created by enzymes which leave a blunt end.

See Also:

Constant Field Values

name

protected String name

site

protected SymbolList site

cutType

protected int cutType

dsCutPositions

protected int[] dsCutPositions

usCutPositions

protected int[] usCutPositions

forwardRegex

protected String forwardRegex

reverseRegex

protected String reverseRegex

Constructor Detail

RestrictionEnzyme

public RestrictionEnzyme(String name,
                 SymbolList site,
                 int dsForward,
                 int dsReverse)
                  throws IllegalAlphabetException

Creates a new RestrictionEnzyme which cuts within or downstream of the recognition site. The cut position indices are always in the same coordinate space as the recognition site. RestrictionEnzymes are immutable.

Parameters:

name - a String such as EcoRI.

site - a SymbolList recognition site.

dsForward - an int index in the forward strand (the strand conventionally written 5'-3') of the recognition site at which the cut occurs. The cut occurs between this base and the following one.

dsReverse - an int index in the reverse strand (the strand conventionally written 3'-5') of the recognition site at which the cut occurs. The cut occurs between this base and the following one.

Throws:

IllegalAlphabetException - if an error occurs.

RestrictionEnzyme

public RestrictionEnzyme(String name,
                 SymbolList site,
                 int usForward,
                 int usReverse,
                 int dsForward,
                 int dsReverse)
                  throws IllegalAlphabetException

Creates a new RestrictionEnzyme of the unusual type which cuts both upstream and downstream of its recognition site. The cut position indices are always in the same coordinate space as the recognition site.

Parameters:

name - a String such as Bsp24I.

site - a SymbolList recognition site.

usForward - an int index in the forward strand (the strand conventionally written 5'-3' upstream of the recognition site at which the cut occurs. The cut occurs between this base and the following one.

usReverse - an int index in the reverse strand (the strand conventionally written 3'-5) upstream of the recognition site at which the cut occurs. The cut occurs between this base and the following one.

dsForward - an int index in the forward strand (the strand conventionally written 5'-3') downstream of the recognition site at which the cut occurs. The cut occurs between this base and the following one.

dsReverse - an int index in the reverse strand (the strand conventionally written 3'-5') downstream of the recognition site at which the cut occurs. The cut occurs between this base and the following one.

Throws:

IllegalAlphabetException - if an error occurs.

Method Detail

getName

public String getName()

getName returns the enzyme name.

Returns:

a String.

getRecognitionSite

public SymbolList getRecognitionSite()

getRecognitionSite returns the forward strand of the recognition site.

Returns:

a SymbolList.

getForwardRegex

public String getForwardRegex()

getForwardRegex returns a regular expression which matches the forward strand of the recognition site.

Returns:

a String.

getReverseRegex

public String getReverseRegex()

getReverseRegex returns a regular expression which matches the reverse strand of the recognition site.

Returns:

a String.

isPalindromic

public boolean isPalindromic()

isPalindromic returns true if the recognition site is palindromic.

Returns:

a boolean.

getCutType

public int getCutType()

getCutType returns the type of cut produced by the enzyme. This will be one of either RestrictionEnzyme.CUT_SIMPLE (where it cuts in one position relative to the recognition site i.e. the vast majority of cases) or RestrictionEnzyme.CUT_COMPOUND (where it cuts in two positions).

Returns:

an int.

getDownstreamCut

public int[] getDownstreamCut()

getDownstreamCut returns the cut site within or downstream of the recognition site.

Returns:

an int [] array with the position in the 5'-strand at index 0 and the 3'-strand at index 1.

getUpstreamCut

public int[] getUpstreamCut()
                     throws BioException

getUpstreamCut returns the cut site upstream of the recognition site.

Returns:

an int [] array with the position in the 5'-strand at index 0 and the 3'-strand at index 1. For example, Bsp24I will return -8 and -13: 5' ^NNNNNNNNGACNNNNNNTGGNNNNNNNNNNNN^ 3' 3' ^NNNNNNNNNNNNNCTGNNNNNNACCNNNNNNN^ 5'

Throws:

BioException - if the enzyme does not cleave on both sides of its recognition site.

getDownstreamEndType

public int getDownstreamEndType()

getDownstreamEndType returns the double-stranded end type produced by the primary (intra-site or downstream) cut.

Returns:

an int equal to one of the constant fields OVERHANG_5PRIME, OVERHANG_3PRIME or BLUNT.

getUpstreamEndType

public int getUpstreamEndType()
                       throws BioException

getUpstreamEndType returns the double-stranded end type produced by the secondary (upstream) cut.

Returns:

an int equal to one of the constant fields OVERHANG_5PRIME, OVERHANG_3PRIME or BLUNT.

Throws:

BioException - if the enzyme does not cleave on both sides of its recognition site.

setProtype

public void setProtype(RestrictionEnzyme proto)

Set the prototype of this RestrictionEnzyme.

Parameters:

proto - an isoschizomer of this enzyme.

getPrototype

public RestrictionEnzyme getPrototype()

The prototype is a RestrictionEnzyme that represents a set of isoshizomers. The choice of the representative/prototype is arbitrary; there is one and only one prototype per set of isoschizomers.

Returns:

A representative isoschisomer or null if prototypes are not defined.

isPrototype

public boolean isPrototype()

getCuttingSize

public double getCuttingSize()

The cutting size of a restriction enzyme is defined has the number of nucleotides that are directly involved in the recognition sequence. The size is ponderated as follow: 1 for a single nucleotide, 1/2 for a degeneracy of 2, 1/4 for a degeneracy of 3, and 0 for any N nucleotides.

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object

toString

public String toString()

Overrides:

toString in class Object