Several forces in recent years have revolutionized the science and practice of molecular biology. Several genomes have now been sequenced and a flood of sequence data produced. Scientists and bioinformaticians have been producing voluminous and high-quality annotations of this data for the past five to ten years. The Internet exploded about the same time as sequencing technologies were heating up. The scientific interest in this topic became high around the same time because of the human genome project.
This short book introduces key concepts in biological sequence analysis as simply as possible. These concepts are illustrated using the BioSeqAnalyzer software developed by the authors for students. Think of this booklet as a combination concepts book and a software user s guide. The software and this booklet may be used for self-study, or in a class on bioinformatics. The booklet and the software take the reader and practicer through most of the important topics in sequence analysis. These are pairwise alignment of sequences, multiple alignment of sequences, alignment of sequences to profiles, building of profile hidden Markov models and alignment of sequences to them, and classification of sequences into groups by composition or by sequence structure. All these features are provided in one software program, in a consistent and easy-to-use interface.
First, we illustrate and practice these concepts with the simplest possible synthetic examples. Next, we use real biological data and subject them to various types of analysis.
The main aim of the authors is to shorten and steepen the learning curve of students as much as possible. This is achieved with the combination of software whose features cover the range of methods used in sequence analysis and provided in a single, consistent, and easy-to-use interface, and the booklet which explains and practices these concepts as simply as possible.
Enjoy!