Combinatorial Computational Biology of RNA Pseudoknots and Neutral N
In this monograph, new combinatorial and computational approaches in the study of RNA structures are presented which enhance both mathematics and computational biology. It begins with an introductory chapter, which motivates and sets the background of thi
- PDF / 8,443,023 Bytes
- 261 Pages / 439.37 x 666.142 pts Page_size
- 93 Downloads / 194 Views
Combinatorial Computational Biology of RNA Pseudoknots and Neutral Networks
Christian Reidys Nankai University Tianjin, China
123
Christian Reidys Research Center for Combinatorics Nankai University Tianjin 300071, China [email protected]
ISBN 978-0-387-76730-7 e-ISBN 978-0-387-76731-4 DOI 10.1007/978-0-387-76731-4 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2010937101
Mathematics Subject Classification (2011): 05-02, 05E10, 05C80, 92-02, 05A15, 05A16 c Springer Science+Business Media, LLC 2011 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com)
Preface
The lack of real contact between mathematics and biology is either a tragedy, a scandal or a challenge, it is hard to decide which. Gian-Carlo Rota, Discrete Thoughts. This book presents the discrete mathematics of RNA pseudoknot structures and their corresponding neutral networks. These structures generalize the extensively studied RNA secondary structures in a natural way by allowing for cross-serial bonds. RNA pseudoknot structures require a completely novel approach which is systematically developed here. After providing the necessary context and background, we give an in-depth combinatorial and probabilistic analysis of these structures, including their uniform generation. We furthermore touch their generation by present the ab initio folding algorithm, cross, freely available at www.combinatorics.cn/cbpc/cross.html. Finally, we analyze the properties of neutral networks of RNA pseudoknot structures. We do not intend to give a complete picture about the state of the theory in RNA folding or computational biology in general. Three decades after the seminal work of Michael Waterman great advances have been made the representation of which is beyond the scope of this book. Instead, we focus on integrating a variety of rather new concepts and ideas, some – if not most – of which originated from pure mathematics and are spread over more than fifty research papers. This book gives graduate students and researchers alike the opportunity to understand in depth the theory of RNA pseudoknot structures and their neutral networks. The book adopts the perspective that mathematical biology is both mathematics and biology in its own right and does not reduce mathema
Data Loading...
