<?xml version="1.0" encoding="ISO-8859-1"?>
<!--To add new enzymes you must define a regex for where they cut, as well a regex
(or a comma separated list of regexes for specificity for multiple successive sites) for what the enzyme cuts after
and what it cuts before. Also be sure to add gains before and after the cut. -->

<PARAMETERS>
  <NODE name="Enzymes">
    <NODE name="RNase_T1">
      <ITEM name="Name" value="RNase_T1" type="string" />
      <ITEM name="RegEx" value="(?&lt;=G)" type="string" />
      <ITEM name="RegExDescription" value="RNase T1 cuts after G." type="string" />
      <ITEM name="CutsAfter" value="G(?!m)" type="string" />
      <ITEM name="CutsBefore" value=".*" type="string" />
      <ITEM name="ThreePrimeGain" value="p" type="string" />
      <ITEM name="FivePrimeGain" value="" type="string" />
    </NODE>
    <NODE name="cusativin">
      <ITEM name="Name" value="cusativin" type="string" />
      <ITEM name="RegEx" value="(?&lt;=C)(?!C)" type="string" />
      <ITEM name="RegExDescription" value="Cusativin cuts after a row of Cs." type="string" />
      <ITEM name="CutsAfter" value="C(?!m)" type="string" />
      <ITEM name="CutsBefore" value="^[^C]+$" type="string" />
      <ITEM name="ThreePrimeGain" value="p" type="string" />
      <ITEM name="FivePrimeGain" value="" type="string" />
    </NODE>
    <NODE name="RNase_U2">
      <ITEM name="Name" value="RNase_U2" type="string" />
      <ITEM name="RegEx" value="(?&lt;=A|G)" type="string" />
      <ITEM name="RegExDescription" value="RNase U2 cuts after A or G." type="string" />
      <ITEM name="CutsAfter" value="G|A(?!m)" type="string" />
      <ITEM name="CutsBefore" value=".*" type="string" />
      <ITEM name="ThreePrimeGain" value="p" type="string" />
      <ITEM name="FivePrimeGain" value="" type="string" />
    </NODE>
    <NODE name="RNase_A">
      <ITEM name="Name" value="RNase_A" type="string" />
      <ITEM name="RegEx" value="(?&lt;=C|U)" type="string" />
      <ITEM name="RegExDescription" value="RNase A cuts after C or U." type="string" />
      <ITEM name="CutsAfter" value="[CUY](?!m)" type="string" />
      <ITEM name="CutsBefore" value=".*" type="string" />
      <ITEM name="ThreePrimeGain" value="p" type="string" />
      <ITEM name="FivePrimeGain" value="" type="string" />
    </NODE>
    <NODE name="RNase_MC1">
      <ITEM name="Name" value="RNase_MC1" type="string" />
      <ITEM name="RegEx" value="(?&lt;=U)" type="string" />
      <ITEM name="RegExDescription" value="RNase MC1 cuts before U." type="string" />
      <ITEM name="CutsAfter" value=".*(?!m)$" type="string" />
      <ITEM name="CutsBefore" value="U|Y" type="string" />
      <ITEM name="ThreePrimeGain" value="p" type="string" />
      <ITEM name="FivePrimeGain" value="" type="string" />
    </NODE>
    <NODE name="RNase_H">
      <ITEM name="Name" value="RNase_H" type="string" />
      <ITEM name="RegEx" value="(?&lt;=.)" type="string" />
      <ITEM name="RegExDescription" value="RNase H can cut anywhere (in an RNA-DNA duplex)." type="string" />
      <ITEM name="CutsAfter" value=".*" type="string" />
      <ITEM name="CutsBefore" value=".*" type="string" />
      <ITEM name="ThreePrimeGain" value="" type="string" />
      <ITEM name="FivePrimeGain" value="p" type="string" />
    </NODE>
    <NODE name="mazF">
      <ITEM name="Name" value="mazF" type="string" />
      <ITEM name="RegEx" value="(?&lt;=(?&lt;!m6)A,(?&lt;!m5)C,A)" type="string" />
      <ITEM name="RegExDescription" value="mazF cuts before ACA but does not cut if the first A is an m6A OR the C is an m5C. NB cleaving behaviour relative to other methylation is not considered" type="string" />
      <ITEM name="CutsAfter" value=".*" type="string" />
      <ITEM name="CutsBefore" value="(?&lt;!m6)A,(?&lt;!m5)C,A" type="string" />
      <ITEM name="ThreePrimeGain" value="p" type="string" />
      <ITEM name="FivePrimeGain" value="" type="string" />
    </NODE>
    <NODE name="colicin_E5">
      <ITEM name="Name" value="colicin_E5" type="string" />
      <ITEM name="RegEx" value="(?&lt;=G|Q)U" type="string" />
      <ITEM name="RegExDescription" value="colicin E5 cuts after G (or Q) followed by U." type="string" />
      <ITEM name="CutsAfter" value="G|Q(?!m)" type="string" />
      <ITEM name="CutsBefore" value="U" type="string" />
      <ITEM name="ThreePrimeGain" value="p" type="string" />
      <ITEM name="FivePrimeGain" value="" type="string" />
    </NODE>
    <NODE name="no cleavage">
      <ITEM name="Name" value="no cleavage" type="string" />
      <ITEM name="RegEx" value="()" type="string" />
      <ITEM name="RegExDescription" value="No cleavage." type="string" />
      <ITEM name="CutsAfter" value="" type="string" />
      <ITEM name="CutsBefore" value="" type="string" />
    </NODE>
    <NODE name="unspecific cleavage">
      <ITEM name="Name" value="unspecific cleavage" type="string" />
      <ITEM name="RegEx" value="(?&lt;=.)" type="string" />
      <ITEM name="RegExDescription" value="Unspecific cleavage cuts at every site." type="string" />
      <ITEM name="CutsAfter" value=".*" type="string" />
      <ITEM name="CutsBefore" value=".*" type="string" />
      <ITEM name="ThreePrimeGain" value="p" type="string" />
      <ITEM name="FivePrimeGain" value="" type="string" />      
    </NODE>
  </NODE>
</PARAMETERS>
