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
||||||||||||||||||| ||||||||
3-NNCCTTCTCATTATGTGAT-TTTNCCNN-5
    ||||||||||||||||| |||
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.