In LoadingBFX/rsrm: Locating restriction sites around specific target sequence and construct restriction map by fragments

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(rsrm)

Introduction

rsrm is a contributed R package for restriction sites mapping for known DNA sequence and construct the restriction map for unkown DNA sequence with given single and double digests reaction result.

Restriction Sites Mapping for Known DNA Sequence

    seq1 <- 'GGCAGATTCCCCCTAACGTCGGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGT
    ATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAGACACC
    ATGAGAGCCCTCACACTCCTCGCCCTATTGGCCCTGGCCGCACTTTGCATCGCTGGCCAGGCAGGTGAGTGCCCC'
    name1 <- 'example DNA Sequence'
    seq2 <- 'ACGTCG'
    name2 <- 'Target'
    result <- findre(name1, seq1, name2, seq2)
    result

Construct Restriction Map for Unkown DNA Sequence

frag1 <- c(100)
frag2 <- c(50, 25, 20, 5)
dou_dig <- c(25, 25, 25, 20, 5)
enz1 <- 'enz1'
enz2 <- 'enz2'
result <- rsmap(enz1, frag1, enz2, frag2, dou_dig)
result

References

Scrucca L., Fop M., Murphy T. B. and Raftery A. E. (2016) mclust 5: clustering, classification and density estimation using Gaussian finite mixture models The R Journal 8/1, pp. 205-233 https://cran.r-project.org/web/packages/mclust/vignettes/mclust.html

LoadingBFX/rsrm documentation built on Dec. 8, 2019, 8:40 a.m.