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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Restriction-module.html">Package Restriction</a> ::
Module Restriction
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<h1 class="epydoc">Module Restriction</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html">source code</a></span></p>
<pre class="literalblock">
Notes about the diverses class of the restriction enzyme implementation.
RestrictionType is the type of all restriction enzymes.
----------------------------------------------------------------------------
AbstractCut implements some methods that are common to all enzymes.
----------------------------------------------------------------------------
NoCut, OneCut,TwoCuts represent the number of double strand cuts
produced by the enzyme.
they correspond to the 4th field of the rebase
record emboss_e.NNN.
0->NoCut : the enzyme is not characterised.
2->OneCut : the enzyme produce one double strand cut.
4->TwoCuts : two double strand cuts.
----------------------------------------------------------------------------
Meth_Dep, Meth_Undep represent the methylation susceptibility to
the enzyme.
Not implemented yet.
----------------------------------------------------------------------------
Palindromic, if the site is palindromic or not.
NotPalindromic allow some optimisations of the code.
No need to check the reverse strand
with palindromic sites.
----------------------------------------------------------------------------
Unknown, Blunt, represent the overhang.
Ov5, Ov3 Unknown is here for symetry reasons and
correspond to enzymes that are not characterised
in rebase.
----------------------------------------------------------------------------
Defined, Ambiguous, represent the sequence of the overhang.
NotDefined
NotDefined is for enzymes not characterised in
rebase.
Defined correspond to enzymes that display a
constant overhang whatever the sequence.
ex : EcoRI. G^AATTC -> overhang :AATT
CTTAA^G
Ambiguous : the overhang varies with the
sequence restricted.
Typically enzymes which cut outside their
restriction site or (but not always)
inside an ambiguous site.
ex :
AcuI CTGAAG(22/20) -> overhang : NN
AasI GACNNN^NNNGTC -> overhang : NN
CTGN^NNNNNCAG
note : these 3 classes refers to the overhang not the site.
So the enzyme ApoI (RAATTY) is defined even if its restriction
site is ambiguous.
ApoI R^AATTY -> overhang : AATT -> Defined
YTTAA^R
Accordingly, blunt enzymes are always Defined even
when they cut outside their restriction site.
----------------------------------------------------------------------------
Not_available, as found in rebase file emboss_r.NNN files.
Commercially_available
allow the selection of the enzymes according to
their suppliers to reduce the quantity
of results.
Also will allow the implementation of buffer
compatibility tables. Not implemented yet.
the list of suppliers is extracted from
emboss_s.NNN
----------------------------------------------------------------------------
</pre>
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<a href="Bio.Restriction.Restriction.FormattedSeq-class.html" class="summary-name">FormattedSeq</a><br />
FormattedSeq(seq, [linear=True])-> new FormattedSeq.
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RestrictionType.
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<a href="Bio.Restriction.Restriction.AbstractCut-class.html" class="summary-name">AbstractCut</a><br />
Implement the methods that are common to all restriction enzymes.
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Implement the methods specific to the enzymes that do not cut.
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<a href="Bio.Restriction.Restriction.OneCut-class.html" class="summary-name">OneCut</a><br />
Implement the methods specific to the enzymes that cut the DNA only
once
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<a href="Bio.Restriction.Restriction.TwoCuts-class.html" class="summary-name">TwoCuts</a><br />
Implement the methods specific to the enzymes that cut the DNA twice
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Implement the information about methylation.
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Implement informations about methylation sensitibility.
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<a href="Bio.Restriction.Restriction.Palindromic-class.html" class="summary-name">Palindromic</a><br />
Implement the methods specific to the enzymes which are palindromic
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<a href="Bio.Restriction.Restriction.NonPalindromic-class.html" class="summary-name">NonPalindromic</a><br />
Implement the methods specific to the enzymes which are not palindromic
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<a href="Bio.Restriction.Restriction.Unknown-class.html" class="summary-name">Unknown</a><br />
Implement the methods specific to the enzymes for which the overhang
is unknown.
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<a href="Bio.Restriction.Restriction.Blunt-class.html" class="summary-name">Blunt</a><br />
Implement the methods specific to the enzymes for which the overhang
is blunt.
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<a href="Bio.Restriction.Restriction.Ov5-class.html" class="summary-name">Ov5</a><br />
Implement the methods specific to the enzymes for which the overhang
is recessed in 3'.
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<a href="Bio.Restriction.Restriction.Ov3-class.html" class="summary-name">Ov3</a><br />
Implement the methods specific to the enzymes for which the overhang
is recessed in 5'.
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<a href="Bio.Restriction.Restriction.Defined-class.html" class="summary-name">Defined</a><br />
Implement the methods specific to the enzymes for which the overhang
and the cut are not variable.
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Implement the methods specific to the enzymes for which the overhang
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Implement the methods specific to the enzymes for which the overhang
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<a href="Bio.Restriction.Restriction.Commercially_available-class.html" class="summary-name">Commercially_available</a><br />
Implement the methods specific to the enzymes which are commercially
available.
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Implement the methods specific to the enzymes which are not
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<a href="Bio.Restriction.Restriction.RestrictionBatch-class.html" class="summary-name">RestrictionBatch</a>
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<a href="Bio.Restriction.Restriction-module.html#matching" class="summary-name">matching</a> = <code title="{'A': 'ARWMHVDN', 'C': 'CYSMHBVN', 'G': 'GRSKBVDN', 'T': 'TYWKHBDN', '\
R': 'ABDGHKMNSRWV', 'Y': 'CBDHKMNSTWVY', 'W': 'ABDHKMNRTWVY', 'S': 'CB\
DGHKMNSRVY', 'M': 'ACBDHMNSRWVY', 'K': 'BDGHKNSRTWVY', 'H': 'ACBDHKMNS\
RTWVY', 'B': 'CBDGHKMNSRTWVY', 'V': 'ACBDGHKMNSRWVY', 'D': 'ABDGHKMNSR\
TWVY', 'N': 'ACBDGHKMNSRTWVY'}">{'A': 'ARWMHVDN', 'C': 'CYSMHBVN', 'G': 'GRSKBVDN',<code class="variable-ellipsis">...</code></code>
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<a name="CommOnly"></a><span class="summary-name">CommOnly</span> = <code title="RestrictionBatch()">RestrictionBatch()</code>
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<a name="NonComm"></a><span class="summary-name">NonComm</span> = <code title="RestrictionBatch()">RestrictionBatch()</code>
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<a name="AllEnzymes"></a><span class="summary-name">AllEnzymes</span> = <code title="CommOnly | NonComm">CommOnly | NonComm</code>
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<h3 class="epydoc">matching</h3>
<dl class="fields">
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<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
{'A': 'ARWMHVDN', 'C': 'CYSMHBVN', 'G': 'GRSKBVDN', 'T': 'TYWKHBDN', '<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
R': 'ABDGHKMNSRWV', 'Y': 'CBDHKMNSTWVY', 'W': 'ABDHKMNRTWVY', 'S': 'CB<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
DGHKMNSRVY', 'M': 'ACBDHMNSRWVY', 'K': 'BDGHKNSRTWVY', 'H': 'ACBDHKMNS<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
RTWVY', 'B': 'CBDGHKMNSRTWVY', 'V': 'ACBDGHKMNSRWVY', 'D': 'ABDGHKMNSR<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
TWVY', 'N': 'ACBDGHKMNSRTWVY'}
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