knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
library(rsrm)
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.
seq1 <- 'GGCAGATTCCCCCTAACGTCGGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGT ATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAGACACC ATGAGAGCCCTCACACTCCTCGCCCTATTGGCCCTGGCCGCACTTTGCATCGCTGGCCAGGCAGGTGAGTGCCCC' name1 <- 'example DNA Sequence' seq2 <- 'ACGTCG' name2 <- 'Target' result <- findre(name1, seq1, name2, seq2) result
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
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
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