RestrictionEnzymeInterface
in
Interface RestrictionEnzymeInterface - substances that can "cut" a DNA strand into two or more fragments along special sites called restriction sites. They are an important tool in recombinant DNA technology.
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Table of Contents
Methods
- cutSeq() : array<string|int, mixed>
- Cuts a DNA sequence into fragments using the restriction enzyme object.
- findRestEn() : array<string|int, mixed>
- A powerful method for searching our database of endonucleases for a particular restriction enzyme exhibiting certain properties like pattern, cutting position, and length, or combinations thereof.
- getCutPos() : int
- Returns the cutting position of the restriction enzyme object.
- getEnzyme() : Enzyme
- getLength() : int
- Returns the length of the cutting pattern of the restriction enzyme object.
- getPattern() : string
- Returns the pattern associated with a given restriction endonuclease.
- parseEnzyme() : mixed
- It creates a new Enzyme object and initializes its properties accordingly.
- setEnzyme() : mixed
- Sets a new enzyme element
- setSequenceManager() : mixed
- Sets a sequence object
Methods
cutSeq()
Cuts a DNA sequence into fragments using the restriction enzyme object.
public
cutSeq([string $options = "N" ]) : array<string|int, mixed>
Sites are searched on both strands, a degenerate (IUPAC) site is matched by every sequence it stands for, and each upper-strand cut position splits the sequence once.
Parameters
- $options : string = "N"
-
May be "N" or "O". If "N", sites overlapping a site already found are ignored. If "O", overlapping sites are cut as well. If omitted, this defaults to "N".
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Return values
array<string|int, mixed> —The fragments, in sequence order : the whole sequence when it holds no site
findRestEn()
A powerful method for searching our database of endonucleases for a particular restriction enzyme exhibiting certain properties like pattern, cutting position, and length, or combinations thereof.
public
findRestEn([string $sPattern = null ][, int $iCutpos = null ][, int $iPlen = null ]) : array<string|int, mixed>
5 Cases: pattern only, cutpos only, patternlength only, pattern and cutpos, cutpos and patternlength
Parameters
- $sPattern : string = null
-
The pattern of the restriction enzyme we wish to look for.
- $iCutpos : int = null
-
The cutting position of the restriction enzyme we wish to look for.
- $iPlen : int = null
-
The length of the restriction enzyme we wish to look for.
Tags
Return values
array<string|int, mixed> —A list of restriction enyzmes that meet the criteria specified by the $pattern, $cutpos, and $plen parameters.
getCutPos()
Returns the cutting position of the restriction enzyme object.
public
getCutPos(string $RestEn_Name) : int
Parameters
- $RestEn_Name : string
Return values
int —Returns the cutting position (an integer) of the restriction enzyme object.
getEnzyme()
public
getEnzyme() : Enzyme
Return values
EnzymegetLength()
Returns the length of the cutting pattern of the restriction enzyme object.
public
getLength([string $RestEn_Name = "" ]) : int
Parameters
- $RestEn_Name : string = ""
Return values
int —The length (integer) of the restriction pattern recognized by the enzyme.
getPattern()
Returns the pattern associated with a given restriction endonuclease.
public
getPattern(string $RestEn_Name) : string
Parameters
- $RestEn_Name : string
Return values
string —The sequence pattern (string) recognized by the given restriction enzyme.
parseEnzyme()
It creates a new Enzyme object and initializes its properties accordingly.
public
parseEnzyme(string $sName[, string $sPattern = null ][, string $sCutpos = null ][, string $sMake = "custom" ]) : mixed
If passed with make = 'custom', object will be added to aRestEnzimDB. If not, the function will attemp to retrieve data from aRestEnzimDB. If unsuccessful in retrieving data, it will return an error flag.
Parameters
- $sName : string
- $sPattern : string = null
- $sCutpos : string = null
- $sMake : string = "custom"
Tags
setEnzyme()
Sets a new enzyme element
public
setEnzyme() : mixed
setSequenceManager()
Sets a sequence object
public
setSequenceManager(SequenceInterface $sequenceManager) : mixed
Parameters
- $sequenceManager : SequenceInterface