The Burrows-Wheeler Transform:: Data Compression, Suffix Arrays, and Pattern Matching

The Burrows-Wheeler Transform is one of the best lossless compression me- ods available. It is an intriguing ― even puzzling ― approach to squeezing redundancy out of data, it has an interesting history, and it has applications well beyond its original purpose as a compression method. It is a relatively late addition to the compression canon, and hence our motivation to write this book, looking at the method in detail, bringing together the threads that led to its discovery and development, and speculating on what future ideas might grow out of it. The book is aimed at a wide audience, ranging from those interested in learning a little more than the short descriptions of the BWT given in st- dard texts, through to those whose research is building on what we know about compression and pattern matching. The ?rst few chapters are a careful description suitable for readers with an elementary computer science ba- ground (and these chapters have been used in undergraduate courses), but later chapters collect a wide range of detailed developments, some of which are built on advanced concepts from a range of computer science topics (for example, some of the advanced material has been used in a graduate c- puter science course in string algorithms). Some of the later explanations require some mathematical sophistication, but most should be accessible to those with a broad background in computer science.

This book will serve as a reference for seasoned professionals or researchers in the area, while remaining accessible for senior undergraduate students or first year graduate students embarking upon research in compression, pattern matching, full text retrieval, compressed index structures, or other areas related to the BWT.

Key features include a comprehensive resource for information related to different aspects of the Burrows-Wheeler Transform, an exploration of non-traditional applications of the BWT in areas such as Bioinformatics, test data compression for systems-on-chip and multimedia information retrieval, and tutorial materials ideal for classroom use.

Advance Praise for The Burrows-Wheeler Transform:

"A thorough discussion of the Burrows-Wheeler Transform and its many connections to pattern-matching and data compression is long overdue. This fascinating, comprehensive monograph fills a gap: a ‘must-read’ for researchers in bioinformatics and computer science".

-- Professor Bill Smyth, McMaster University, Canada

"A much-needed book providing the first complete coverage of the principles and applications of a fascinating tool. The exposition is rigorous but still easy to follow. I heartily recommend this book to anyone interested in data compression or string algorithms".

-- Professor Giovanni Manzini, Università del Piemonte Orientale, Italy