Chapter 2 - Protein Sequence Analysis

Abstract

This chapter discusses the protein sequence analysis. The analysis of protein sequences provides the information about the preference of amino acid residues and their distribution along the sequences for understanding the secondary and tertiary structures of proteins and their functions. The identification of similar motifs in protein sequences would help to predict the structurally or functionally important regions. The profiles obtained with the single amino acid properties based on amino acid sequence would reveal the clustering of amino acids with similar property. Amino acid sequences have a lot of hidden information, which can be used for developing sequence-based prediction methods. The comparison of different amino acid sequences using alignment methods would enhances the knowledge about the availability of similar sequences, and these sequences could be used as a template for protein three-dimensional structure prediction. Aligning the sequences or structures mainly carries out the comparison of two proteins. In this method, a one-to-one correspondence is set up between the residues of the two proteins. The simplest observation is the global alignment of two sequences, in which the two proteins have maintained a correspondence over the entire length. An alternative is the local alignment in which the alignment is made only with the most similar part of the proteins.