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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 ----------------------------------------------------------------------------
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enzymedict =
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typedict =
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suppliers_dict =
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matching =
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CommOnly = RestrictionBatch(['AanI', 'AarI', 'AasI', 'AatI', '
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NonComm = RestrictionBatch(['AceIII', 'AhaIII', 'AlwFI', 'ApaB
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AllEnzymes = RestrictionBatch(['AanI', 'AarI', 'AasI', 'AatI',
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ConsoleWidth = 80
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Indent = 4
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MaxSize = 6
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NameWidth = 10
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Rebase_name =
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Rebase_password =
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__package__ =
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ftp_Rebase =
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ftp_emb_e =
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ftp_emb_r =
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ftp_emb_s =
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ftp_proxy =
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Check characters in a string (PRIVATE). Remove digits and white space present in string. Allows any valid ambiguous IUPAC DNA single letters codes (ABCDGHKMNRSTVWY, lower case are converted). Other characters (e.g. symbols) trigger a TypeError. Returns the string WITH A LEADING SPACE (!). This is for backwards compatibility, and may in part be explained by the fact that Bio.Restriction doesn't use zero based counting. |
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enzymedict
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typedict
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suppliers_dict
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matching
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CommOnly
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NonComm
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AllEnzymes
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