biopython v1.71.0 Bio.Restriction.Restriction

Restriction Enzyme classes.

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 symmetry reasons and
                                correspond to enzymes that are not
                                characterised in rebase.
        Defined, Ambiguous,     represent the sequence of the overhang.
                                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

                                Ambiguous : the overhang varies with the
                                sequence restricted.
                                Typically enzymes which cut outside their
                                restriction site or (but not always)
                                inside an ambiguous site.
                                AcuI CTGAAG(22/20)  -> overhang : NN
                                AasI GACNNN^NNNGTC  -> overhang : NN

            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
               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.
                                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

Link to this section Summary


Check characters in a string (PRIVATE)

Link to this section Functions

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.