Package Bio :: Package Restriction :: Module Restriction :: Class Ov5
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Type Ov5

source code

 object --+            
          |            
       type --+        
              |        
RestrictionType --+    
                  |    
        AbstractCut --+
                      |
                     Ov5
Known Subclasses:

Implement the methods specific to the enzymes for which the overhang is recessed in 3'.

The enzyme cuts the + strand after the - strand of the DNA.

Internal use only. Not meant to be instantiated.

Instance Methods [hide private]

Inherited from RestrictionType: __add__, __div__, __eq__, __floordiv__, __ge__, __gt__, __hash__, __init__, __le__, __len__, __lt__, __mod__, __ne__, __rdiv__, __repr__, __rfloordiv__, __rshift__, __rtruediv__, __str__, __truediv__

Inherited from type: __call__, __delattr__, __getattribute__, __new__, __setattr__, __subclasses__, mro

Inherited from object: __format__, __reduce__, __reduce_ex__, __sizeof__, __subclasshook__

Class Methods [hide private]
tuple of DNA
catalyse(RE, dna, linear=True)
RE.catalyze(dna, linear=True) -> tuple of DNA.
source code
tuple of DNA
catalyze(RE, dna, linear=True)
RE.catalyze(dna, linear=True) -> tuple of DNA.
source code
bool
is_blunt(RE)
True if the enzyme produces blunt end.
source code
bool
is_5overhang(RE)
True if the enzyme produces 5' overhang sticky end.
source code
bool
is_3overhang(RE)
True if the enzyme produces 3' overhang sticky end.
source code
str
overhang(RE)
type of overhang of the enzyme.,
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list
compatible_end(RE)
list of all the enzymes that share compatible end with RE.
source code
bool
_mod1(RE, other)
for internal use only
source code

Inherited from AbstractCut: all_suppliers, equischizomers, frequency, is_equischizomer, is_isoschizomer, is_neoschizomer, isoschizomers, neoschizomers, search

Properties [hide private]

Inherited from type: __abstractmethods__, __base__, __bases__, __basicsize__, __dictoffset__, __flags__, __instancecheck__, __itemsize__, __mro__, __name__, __subclasscheck__, __weakrefoffset__

Inherited from object: __class__

Method Details [hide private]

catalyse(RE, dna, linear=True)
Class Method

source code 

RE.catalyze(dna, linear=True) -> tuple of DNA.

return a tuple of dna as will be produced by using RE to restrict the dna.

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

if linear is False, the sequence is considered to be circular and the output will be modified accordingly.

Returns: tuple of DNA

catalyze(RE, dna, linear=True)
Class Method

source code 

RE.catalyze(dna, linear=True) -> tuple of DNA.

return a tuple of dna as will be produced by using RE to restrict the dna.

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

if linear is False, the sequence is considered to be circular and the output will be modified accordingly.

Returns: tuple of DNA

is_blunt(RE)
Class Method

source code 

True if the enzyme produces blunt end.

see also:
RE.is_3overhang() RE.is_5overhang() RE.is_unknown()
Returns: bool

is_5overhang(RE)
Class Method

source code 

True if the enzyme produces 5' overhang sticky end.

see also:
RE.is_3overhang() RE.is_blunt() RE.is_unknown()
Returns: bool

is_3overhang(RE)
Class Method

source code 

True if the enzyme produces 3' overhang sticky end.

see also:
RE.is_5overhang() RE.is_blunt() RE.is_unknown()
Returns: bool

overhang(RE)
Class Method

source code 

type of overhang of the enzyme.,

can be "3' overhang", "5' overhang", "blunt", "unknown"

Returns: str

_mod1(RE, other)
Class Method

source code 

for internal use only

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

Returns: bool