biopython

v1.71.0

biopython v1.71.0 Bio.Restriction.Restriction.Defined

Implement methods for enzymes with defined recognition site and cut.

Typical example : EcoRI -> G^AATT_C

              The overhang will always be AATT

Notes:

Blunt enzymes are always defined. Even if their site is GGATCCNNN^_N
Their overhang is always the same : blunt!

Internal use only. Not meant to be instantiated.

Link to this section Summary

Functions

_drop()

Remove cuts that are outsite of the sequence (PRIVATE)

_mod2()

Test if other enzyme produces compatible ends for enzyme (PRIVATE)

elucidate()

Return a string representing the recognition site and cuttings

is_ambiguous()

Return if recognition sequence and cut may be ambiguous

is_defined()

Return if recognition sequence and cut are defined

is_unknown()

Return if recognition sequence is unknown

Link to this section Functions

Link to this function _drop()

Remove cuts that are outsite of the sequence (PRIVATE).

For internal use only.

Drop the site that are situated outside the sequence in linear sequence. Modify the index for site in circular sequences.

Link to this function _mod2()

Test if other enzyme produces compatible ends for enzyme (PRIVATE).

For internal use only.

Test for the compatibility of restriction ending of RE and other.

Link to this function elucidate()

Return a string representing the recognition site and cuttings.

Return a representation of the site with the cut on the (+) strand represented as ‘^’ and the cut on the (-) strand as ‘_’. ie:

 >>> EcoRI.elucidate()   
 'G^AATT_C'
 >>> KpnI.elucidate()    
 'G_GTAC^C'
 >>> EcoRV.elucidate()   
 'GAT^_ATC'
 >>> SnaI.elucidate()    
 '? GTATAC ?'
 >>>
Link to this function is_ambiguous()

Return if recognition sequence and cut may be ambiguous.

True if the sequence recognised and cut is ambiguous, i.e. the recognition site is degenerated AND/OR the enzyme cut outside the site.

Related methods:

  • RE.is_defined()
  • RE.is_unknown()
Link to this function is_defined()

Return if recognition sequence and cut are defined.

True if the sequence recognised and cut is constant, i.e. the recognition site is not degenerated AND the enzyme cut inside the site.

Related methods:

  • RE.is_ambiguous()
  • RE.is_unknown()
Link to this function is_unknown()

Return if recognition sequence is unknown.

True if the sequence is unknown, i.e. the recognition site has not been characterised yet.

Related methods:

  • RE.is_defined()
  • RE.is_ambiguous()