In order to study living organisms, scientists not only study them at an overall macroscopic scale but also on a more detailed microscopic scale. This observation, pushed to its limits, consists of investigating the very center of each cell, where we find the molecules that determine the way it functions: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
In an organism, DNA carries the genetic information, which is called the genome. It is represented as four-letter sequences using the letters A, C, G and T; based on these sequences, computer methods described in this book can answer fundamental questions in bioinformatics.
This book explores how to quickly find sequences of a few hundred nucleotides within a genome that may be made up of several billion, how to compare those sequences and how to reconstruct the complete sequence of a genome. It also discusses the problems of identifying bacteria in a given environment and predicting the structure of RNA based on its sequence.
1. Methodological Concepts: Algorithmic Solutions of Bioinformatics Problems, Annie Chateau and Tom Davot-Grangé.
2. Sequence Indexing, Thierry Lecroq and Mickaël Salson.
3. Sequence Alignment, Laurent Noé.
4. Genome Assembly, Dominique Lavenier.
5. Metagenomics and Metatranscriptomics, Cervin Guyomar and Claire Lemaitre.
6. RNA Folding, Yann Ponty and Vladimir Reinharz.
Annie Chateau is a lecturer at the University of Montpellier, France. Her research interests include algorithms and combinatorial structures.
Mikaël Salson is a lecturer at the University of Lille, France. His work focuses mainly on indexing and sequence comparison.
Table of Contents
PDF File 64 Kb