Procedure

1.  Follow ( https://vlab.amrita.edu/index.php?sub=3&brch=311&sim=1835&cnt=2) to install R in personal computer.
2. Install the Biostrings package with the commands. 

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

        3. Load the package 

                        require(Biostrings)

Procedure to Work Simulator

1.  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