Pairwise sequence alignment of Protein or DNA sequences

• Follow ( https://vlab.amrita.edu/index.php?sub=3&brch=311&sim=1835&cnt=2) to install R in personal computer.

• Install the Biostrings package with the commands.

                    source("http://bioconductor.org/biocLite.R")
                              biocLite("Biostrings")
          

 

• Load the package

                    require(Biostrings)
                              
          

 

Procedure to Work Simulator

 

Follow the command on R platform

    library(Biostrings)
              sigma <- nucleotideSubstitutionMatrix(match = 2, mismatch = -1, baseOnly = TRUE)
              sigma # Print out the matrix
              s1 <- "GAATTC"
              s2 <- "GATTA"
              globalAligns1s2 <- pairwiseAlignment(s1, s2, substitutionMatrix = sigma,gapOpening = -2, gapExtension = -8,          scoreOnly = FALSE)
              globalAligns1s2