Developing a Bioinformatics Tool

Abstract

This chapter guides through the development of a pairwise sequence alignment tool that implements global, ends-free global, and local alignment. It focuses on the algorithms needed to implement the tool. However, because Python is a commonly used programming language for bioinformatics, the chapter encourages you to apply the Python concepts to implement your pairwise sequence alignment tool. The chapter begins by analysing the output report of an existing local sequence alignment tool, EMBOSS Water, to familiarize ourselves with its inputs, outputs, and functionality. It then looks at an overview of simple pairwise alignment (SPA), and introduces the concept of algorithms–taking a look at different ways to express algorithms. Towards the end, the chapter explains the longest common subsequence (LCS) algorithm and how it can be extended to implement local and global pairwise alignment. It then assesses the complexity of algorithms–that is, how much memory and time they require.