pydna.crispr

Provides the Dseq class for handling double stranded DNA sequences.

Dseq is a subclass of Bio.Seq.Seq. The Dseq class is mostly useful as a part of the pydna.dseqrecord.Dseqrecord class which can hold more meta data.

The Dseq class support the notion of circular and linear DNA topology.

class pydna.crispr.cas9(protospacer)

Bases: _cas

docstring.

|----size----------|

—protospacer——

-fst3

fst5 |-| |--------------|

PAM

5-NNGGAAGAGTAATACACTA-AAANGGNN-3

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3-NNCCTTCTCATTATGTGAT-TTTNCCNN-5

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5-GGAAGAGTAATACACTA-AAAg-u-a-a-g-g Scaffold

—gRNA spacer— u-a

u-a u-a u-a a-u g-u-g

a a

g-c-a c-g u-a a-u

g a tetraloop

a-a

scaffold = 'GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGG'

pam = '.GG'

size = 20

fst5 = 17

fst3 = -3

ovhg = 0

search(dna, linear=True)

docstring.

pydna.crispr.protospacer(guide_construct, cas=cas9)

docstring.