biopython

v1.71.0

biopython v1.71.0 Bio.Restriction.Restriction.AbstractCut

Implement the methods that are common to all restriction enzymes.

All the methods are classmethod.

For internal use only. Not meant to be instantiated.

Link to this section Summary

Functions

all_suppliers()

Print all the suppliers of restriction enzyme

equischizomers()

List equischizomers of the enzyme

frequency()

Return the theoretically cutting frequency of the enzyme

is_equischizomer()

Test for real isoschizomer

is_isoschizomer()

Test for same recognition site

is_neoschizomer()

Test for neoschizomer

isoschizomers()

List all isoschizomers of the enzyme

neoschizomers()

List neoschizomers of the enzyme

search()

Return a list of cutting sites of the enzyme in the sequence

Link to this section Functions

Link to this function all_suppliers()

Print all the suppliers of restriction enzyme.

Link to this function equischizomers()

List equischizomers of the enzyme.

Return a tuple of all the isoschizomers of RE. If batch is supplied it is used instead of the default AllEnzymes.

Equischizomer: same site, same position of restriction.

Link to this function frequency()

Return the theoretically cutting frequency of the enzyme.

Frequency of the site, given as ‘one cut per x bases’ (int).

Link to this function is_equischizomer()

Test for real isoschizomer.

True if other is an isoschizomer of RE, but not an neoschizomer, else False.

Equischizomer: same site, same position of restriction.

 >>> SacI.is_equischizomer(SstI)
 True
 >>> SmaI.is_equischizomer(XmaI)
 False
Link to this function is_isoschizomer()

Test for same recognition site.

True if other has the same recognition site, else False.

Isoschizomer: same site.

 >>> SacI.is_isoschizomer(SstI)
 True
 >>> SmaI.is_isoschizomer(XmaI)
 True
Link to this function is_neoschizomer()

Test for neoschizomer.

True if other is an isoschizomer of RE, else False. Neoschizomer: same site, different position of restriction.

Link to this function isoschizomers()

List all isoschizomers of the enzyme.

Return a tuple of all the equischizomers and neoschizomers of RE. If batch is supplied it is used instead of the default AllEnzymes.

Link to this function neoschizomers()

List neoschizomers of the enzyme.

Return a tuple of all the neoschizomers of RE. If batch is supplied it is used instead of the default AllEnzymes.

Neoschizomer: same site, different position of restriction.

Link to this function search()

Return a list of cutting sites of the enzyme in the sequence.

Compensate for circular sequences and so on.

dna must be a Bio.Seq.Seq instance or a Bio.Seq.MutableSeq instance.

If linear is False, the restriction sites that span over the boundaries will be included.

The positions are the first base of the 3’ fragment, i.e. the first base after the position the enzyme will cut.