Basic Applied Bioinformatics

CHAPTER 6Nucleotide Sequence Analysis Using Sequence Manipulation Suite (SMS)

CS Mukhopadhyay and RK Choudhary

School of Animal Biotechnology, GADVASU, Ludhiana

6.1 INTRODUCTION

Nucleotide and amino acid sequences are analyzed to understand their hidden features, to discover patterns, and to determine function, structure and their evolution. The frequently used in silico analyses using molecular sequences are: sequence alignment; determining conserved regions; identification of low‐complexity region of nucleotides; gene prediction; nucleotide sequence assembling; exploring biochemical and immunogenic properties of amino acid sequences; protein structure prediction, and so on. After completing this chapter, you will learn how to use some of the sequence analytical techniques using free online software called Sequence Manipulation Suite. The original examples cited in the software suit (as “help” for explaining the programs) have been used here. In some places, the explanations may be verbatim.

6.1.1 Sequence Manipulation Suite (SMS)

This is a collection (which is why it is called a “suite”) of software, written in JavaScript1.5, for generating, formatting, and analyzing short DNA and protein sequences. Paul Stothard (of the University of Alberta, Canada) wrote the software suite (Stothard, 2000). The off‐line suite can be downloaded from the link http://www.bioinformatics.org/sms2/mirror.html/.

Sequences are submitted to the sequence box of SMS and then analyzed according to ...