Direct Suffix Sorting

ISBN-13: 9783639101539 / Angielski / Miękka / 2008 / 108 str.

Fei Nan

Opis

Pattern matching plays a central role in different aspects of biological sequence analysis, and has been used in applications as diverse as short-gun sequencing, multiple sequence alignments, gene finding, analysis of repetition structures, searching for unique oligonucleotides, prediction of protein function and structure, sequence homology search, finding DNA-binding protein motifs, etc. Suffix trees and suffix arrays are primary data structures used in rapid pattern matching. And the problem of suffix sorting is a fundamental problem in constructing suffix arrays. This book presents the basics, concepts of suffix trees, suffix arrays and suffix sorting and proposes a direct suffix sorting algorithm which rearranges the biological sequences of interests and facilitate high throughput pattern query, retrieval and storage in linear time. The direct suffix sorting algorithm is then applied to solve practical problems in multiple sequence alignment and data compression. The book serves both as reference for computer scientists, computational biologists and bio-informatic professionals and an essential study materials for graduate and advanced courses on computational biology.

O autorze

Ph.D.: Computer Science at West Virginia University
(2008), M.S.: Microbiology and Immunology at West Virginia
University (2008), B.Eng.: Computer Science at Northeastern
University (2002). Member of Sigma Xi, IEEE and ACM. Software
Engineer at Microsoft Corporation, Redmond, Washington.