Basic Applied Bioinformatics

CHAPTER 8Dot Plot Analysis

CS Mukhopadhyay and RK Choudhary

School of Animal Biotechnology, GADVASU, Ludhiana

8.1 INTRODUCTION

A two‐dimensional (2D) plot depicting one or more of the various sequence features (sequence similarities, direct and/or inverted repeats, motifs, gaps, sequence inversions, etc.) is called a dot plot. A single sequence, or two different sequences (with the same type of residues), can be studied to reveal the hidden sequence features. Dot plot has been used for local (not global) alignment, and was identified as a very powerful tool for molecular sequence analysis as early as during the late 1960s (Fitch, 1969).

8.2 OBJECTIVE

To compare two homologous molecular sequences using a dot plot.

8.3 PROCEDURE

Molecular sequences can be subjected to dot plot analysis using online tools like Dotlet, Dotter, and so on.

1. Dotlet (http://myhits.isb‐sib.ch/util/dotlet/doc/dotlet_help.html). This is freely available online and is used as a tool for diagonal plotting of sequences.
2. Dot plot(+) (http://www.hku.hk/bruhk/gcgdoc/dot plot.html). Dot plot(+) software can identify the overlapping portions of two sequences, and also any repeats and inverted repeats of a particular sequence.
3. Dotter (http://sonnhammer.sbc.su.se/Dotter.html). A graphical dot plot program for thorough comparison of two molecular sequences. Dotter can be run on any of the following operating systems: MAC, Linux, Sun Solaris and Windows OS.

Two different sequences, or a single sequence, can be ...