Chapter 3 - Biological sequence analysis

Abstract

The biological information is stored in the form of DNA, RNA, or proteins. These biomolecules are purported to be acquainted with a unique code of life. Bioinformatics and computational biology fields include essential operation as biological sequence alignment, which has important application in disease diagnosis, biomaterial engineering, genetic engineering, and drug discovery. The score is assigned for the similarity or correlation in alignment, either pairwise alignment or multiple sequence alignment. Based on that score, the degree of similarity is adjudicated and inferred that the sequences are related or distant. Algorithms, such as dynamic programming, greedy method, and genetic algorithms, make the alignment quick and accurate. With the advancement of sequencing techniques, the data size is increasing, researchers along with parallel processing and distributed file systems are using modern tools to ease the process of alignment. This chapter discusses the basics of sequence alignment, algorithms, and tools available for biological sequence alignment.