PAM_pattern: PAM patterns

In CicciaLab/iSTOP: iSTOP - Induced STOP Experiment Design

Description

Specify PAM patterns for use with locate_PAM

Usage

PAM_pattern(pattern, width)

PAM_patterns_default(
  sgNGG = PAM_pattern(".GG", 3),
  sgNGA = PAM_pattern(".GA", 3),
  sgNGCG = PAM_pattern(".GCG", 4),
  sgNGAG = PAM_pattern(".GAG", 4),
  sgNNGRRT = PAM_pattern("..G[AG][AG]T", 6),
  sgNNNRRT = PAM_pattern("...[AG][AG]T", 6),
  ...
)

Arguments

pattern	A regular expression used to identify a PAM. See the regex documentation for extensive help on regular expressions.
width	A single number indicating the expected width of the PAM sequence.
sgNGG	Pattern for NGG. Defaults to PAM_pattern(".GG", 3)
sgNGA	Pattern for NGA. Defaults to PAM_pattern(".GA", 3)
sgNGCG	Pattern for NGCG. Defaults to PAM_pattern(".GCG", 4)
sgNGAG	Pattern for NGAG. Defaults to PAM_pattern('.GAG', 4)
sgNNGRRT	Pattern for NNGRRT. Defaults to PAM_pattern('..G[AG][AG]T', 6)
sgNNNRRT	Pattern for NNNRRT. Defaults to PAM_pattern('...[AG][AG]T', 6)
...	Additional PAM patterns to include in PAM_patterns_default()

CicciaLab/iSTOP documentation built on May 9, 2021, 4:55 p.m.