In rsimon64/bioinfodem:

Init

knitr::opts_chunk$set(echo = TRUE)

Definir secuencias

• seq1
• seq2
• seq3

library(Biostrings)

 s1 <- 
    DNAString("ACTTCACCAGCTCCCTGGCGGTAAGTTGATCAAAGGAAACGCAAAGTTTTCAAG")
  s2 <-
    DNAString("GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC")

  # First use a fixed substitution matrix
  mat <- nucleotideSubstitutionMatrix(match = 1, mismatch = -3, baseOnly = TRUE)


  mat

  localAlign <-
    pairwiseAlignment(s1, s2, type = "local", substitutionMatrix = mat,
                      gapOpening = 5, gapExtension = 2)

  as.character(localAlign)

  aligned(subject(localAlign))

  globalAlign <-
    pairwiseAlignment(s1, s2, substitutionMatrix = mat,
                      gapOpening = 5, gapExtension = 2)

as.character(globalAlign)

rsimon64/bioinfodem documentation built on May 9, 2019, 8:18 a.m.