function __construct Is the constructor method for the Restriction class. It creates a new RestrictionEnzyme object and initializes its properties accordingly.

If passed with make = 'custom', object will be added to Restriction_DB. If not, the function will attempt to retrieve data from Restriction_DB. If unsuccessful in retrieving data, it will return an error flag.

• $aEnzymeProperties

Bio::__construct()

function Bio ()

cutter

getIsoschizomers

getIsPrototype

getMicrobe

getPrototypeName

getRevCompSite

site Gets the recognition sequence for the enzyme.

Side effect: the sequence is always converted to upper case. The cut site can also be set by using methods L<cut|cut> and L<complementary_cut|complementary_cut>. This will pad out missing sequence with N's. For example the enzyme Acc36I cuts at ACCTGC(4/8). This will be returned as ACCTGCNNNN^ Note that the common notation ACCTGC(4/8) means that the forward strand cut is four nucleotides after the END of the recognition site. The forward cut() in the coordinates used here in Acc36I ACCTGC(4/8) is at 6+4 i.e. 10. This is the main setable method for the recognition site.

• return: string containing recognition sequence indicating cleavage site as in 'G^AATTC'.

getVendors

overhang

purgeIsoschizomers

purgeReferences

setCut

• $iCut

setIsPallindromic

• $bIsPallindromic

setMethylationSites

• $aMethylationSites

setName

Sets the restriction enzyme name This will also clean up the name. I have added this because some people get confused about restriction enzyme names. The name should be One upper case letter, and two lower case letters (because it is derived from the organism name, eg. EcoRI is from E. coli). After that it is all confused, but the numbers should be roman numbers not numbers, therefore we'll correct those. At least this will provide some standard, I hope.

• Corrects & sets the restriction enzyme name
• Overrides Seq->setName()
  1. $re->name('EcoRI')

• return: void

• string $sName

setReferences

• $aReferences

setRevCompSite

site Sets the recognition sequence for the enzyme.

Side effect: the sequence is always converted to upper case. The cut site can also be set by using methods L<cut|cut> and L<complementary_cut|complementary_cut>. This will pad out missing sequence with N's. For example the enzyme Acc36I cuts at ACCTGC(4/8). This will be returned as ACCTGCNNNN^ Note that the common notation ACCTGC(4/8) means that the forward strand cut is four nucleotides after the END of the recognition site. The forward cut() in the coordinates used here in Acc36I ACCTGC(4/8) is at 6+4 i.e. 10. This is the main setable method for the recognition site.

• return: string containing recognition sequence indicating cleavage site as in 'G^AATTC'.

• string $sSite

setVendors

• $aVendors

type