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object --+ | type --+ | RestrictionType --+ | AbstractCut --+ | Ambiguous
Implement the methods specific to the enzymes for which the overhang is variable. Typical example : BstXI -> CCAN_NNNN^NTGG The overhang can be any sequence of 4 bases. Notes: Blunt enzymes are always defined. even if there site is GGATCCNNN^_N There overhang is always the same : blunt! Internal use only. Not meant to be instantiated.
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for internal use only. drop the site that are situated outside the sequence in linear sequence. modify the index for site in circular sequences.
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True if the sequence recognised and cut is constant, i.e. the recognition site is not degenerated AND the enzyme cut inside the site. see also: RE.is_ambiguous() RE.is_unknown()
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True if the sequence recognised and cut is ambiguous, i.e. the recognition site is degenerated AND/OR the enzyme cut outside the site. see also: RE.is_defined() RE.is_unknown()
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True if the sequence is unknown, i.e. the recognition site has not been characterised yet. see also: RE.is_defined() RE.is_ambiguous()
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for internal use only test for the compatibility of restriction ending of RE and other.
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return a representation of the site with the cut on the (+) strand represented as '^' and the cut on the (-) strand as '_'. ie: >>> EcoRI.elucidate() # 5' overhang 'G^AATT_C' >>> KpnI.elucidate() # 3' overhang 'G_GTAC^C' >>> EcoRV.elucidate() # blunt 'GAT^_ATC' >>> SnaI.elucidate() # NotDefined, cut profile unknown. '? GTATAC ?' >>>
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