Programming Global and Local Sequence Alignment by Using R

Abstract

R [2] is a programming language primarily oriented to statistical and graphical analysis. Since R is an open source language, new functions of very different fields are continuously appearing all around the world. Operations Research is a multidisciplinary science and given the interest that exists between teachers and researchers to develop procedures that can be applied across the board by students, professionals and scientists, the use of R is needed to solve problems related to the optimization of a system. Dynamic Programming algorithms are essential basis for the development of algorithms that solve other problems. One of the main research areas in Bioinformatics is Sequence Alignment of nucleotide or amino acid residues to identify regions of similarity. The Bioconductor project [3] provides R packages for the analysis of genomic data. This work focuses on alignment of pairs. We develop two functions with R code: localAlignment and globalAlignment. These functions solve standard problems of Local and Global Sequence Alignment by using Dynamic Programming. © Springer-Verlag Berlin Heidelberg 2014.