algorithms on strings trees and sequences computer science and computational biology

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Algorithms On Strings Trees And Sequences

Author : Dan Gusfield
ISBN : 0521585198
Genre : Computers
File Size : 82. 59 MB
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String algorithms are a traditional area of study in computer science. In recent years their importance has grown dramatically with the huge increase of electronically stored text and of molecular sequence data (DNA or protein sequences) produced by various genome projects. This 1997 book is a general text on computer algorithms for string processing. In addition to pure computer science, the book contains extensive discussions on biological problems that are cast as string problems, and on methods developed to solve them. It emphasises the fundamental ideas and techniques central to today's applications. New approaches to this complex material simplify methods that up to now have been for the specialist alone. With over 400 exercises to reinforce the material and develop additional topics, the book is suitable as a text for graduate or advanced undergraduate students in computer science, computational biology, or bio-informatics. Its discussion of current algorithms and techniques also makes it a reference for professionals.

Advances In Computers

Author : Marvin Zelkowitz
ISBN : 0080951112
Genre : Computers
File Size : 81. 34 MB
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This is volume 75 of Advances in Computers. This series, which began publication in 1960, is the oldest continuously published anthology that chronicles the ever- changing information technology field. In these volumes we publish from 5 to 7 chapters, three times per year, that cover the latest changes to the design, development, use and implications of computer technology on society today. In this present volume we present five chapters describing new technology affecting users of such machines. In this volume we continue a theme presented last year in volume 72 – High Performance Computing. In volume 72 we described several research projects being conducted in the United States on the development of a new generation of high performance supercomputers.

Theoretical Computer Science

Author : Mario Coppo
ISBN : 3540291067
Genre : Computers
File Size : 90. 8 MB
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This book constitutes the refereed proceedings of the 9th International Conference on Theoretical Computer Science, ICTCS 2005, held at the Certosa di Pontignano, Siena, Italy, in October 2005. The 29 revised full papers presented together with an invited paper and abstracts of 2 invited talks were carefully reviewed and selected from 83 submissions. The papers address all current issues in theoretical computer science and focus especially on analysis and design of algorithms, computability, computational complexity, cryptography, formal languages and automata, foundations of programming languages and program analysis, natural computing paradigms (quantum computing, bioinformatics), program specification and verification, term rewriting, theory of logical design and layout, type theory, security, and symbolic and algebraic computation.

Combinatorial Pattern Matching Algorithms In Computational Biology Using Perl And R

Author : Gabriel Valiente
ISBN : 1420069748
Genre : Science
File Size : 78. 93 MB
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Emphasizing the search for patterns within and between biological sequences, trees, and graphs, Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R shows how combinatorial pattern matching algorithms can solve computational biology problems that arise in the analysis of genomic, transcriptomic, proteomic, metabolomic, and interactomic data. It implements the algorithms in Perl and R, two widely used scripting languages in computational biology. The book provides a well-rounded explanation of traditional issues as well as an up-to-date account of more recent developments, such as graph similarity and search. It is organized around the specific algorithmic problems that arise when dealing with structures that are commonly found in computational biology, including biological sequences, trees, and graphs. For each of these structures, the author makes a clear distinction between problems that arise in the analysis of one structure and in the comparative analysis of two or more structures. He also presents phylogenetic trees and networks as examples of trees and graphs in computational biology. This book supplies a comprehensive view of the whole field of combinatorial pattern matching from a computational biology perspective. Along with thorough discussions of each biological problem, it includes detailed algorithmic solutions in pseudo-code, full Perl and R implementation, and pointers to other software, such as those on CPAN and CRAN.

Hidden Markov Models For Bioinformatics

Author : T. Koski
ISBN : 1402001363
Genre : Mathematics
File Size : 81. 50 MB
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The purpose of this book is to give a thorough and systematic introduction to probabilistic modeling in bioinformatics. The book contains a mathematically strict and extensive presentation of the kind of probabilistic models that have turned out to be useful in genome analysis. Questions of parametric inference, selection between model families, and various architectures are treated. Several examples are given of known architectures (e.g., profile HMM) used in genome analysis. Audience: This book will be of interest to advanced undergraduate and graduate students with a fairly limited background in probability theory, but otherwise well trained in mathematics and already familiar with at least some of the techniques of algorithmic sequence analysis.

String Processing And Information Retrieval

Author : Edleno Moura
ISBN : 9783319119182
Genre : Computers
File Size : 54. 16 MB
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This book constitutes the proceedings of the 21st International Symposium on String Processing and Information Retrieval, SPIRE 2014, held in Ouro Preto, Brazil, in October 2014. The 20 full and 6 short papers included in this volume were carefully reviewed and selected from 45 submissions. The papers focus not only on fundamental algorithms in string processing and information retrieval, but address also application areas such as computational biology, Web mining and recommender systems. They are organized in topical sections on compression, indexing, genome and related topics, sequences and strings, search, as well as on mining and recommending.

Sequence Evolution Function

Author : Eugene Koonin
ISBN : 1402072740
Genre : Science
File Size : 71. 79 MB
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Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.

Data Mining In Bioinformatics

Author : Jason T. L. Wang
ISBN : 9781846280597
Genre : Computers
File Size : 77. 81 MB
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Written especially for computer scientists, all necessary biology is explained. Presents new techniques on gene expression data mining, gene mapping for disease detection, and phylogenetic knowledge discovery.

Algorithm Theory Swat 2000

Author : Magnus M. Halldorsson
ISBN : UOM:39015048220423
Genre : Algorithms
File Size : 48. 26 MB
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This book constitutes the refereed proceedings of the 7th Scandinavian Workshop on Algorithm Theory, SWAT 2000, held in Bergen, Norway, in July 2000. The 43 revised full papers presented together with 3 invited contributions were carefully reviewed and selected from a total of 105 submissions. The papers are organized in sections on data structures, dynamic partitions, graph algorithms, online algorithms, approximation algorithms, matchings, network design, computational geometry, strings and algorithm engineering, external memory algorithms, optimization, and distributed and fault-tolerant computing.

Proceedings Of The Annual International Conference On Computational Molecular Biology

Author : Dan Gusfield
ISBN : 1581137559
Genre : Molecular biology
File Size : 29. 41 MB
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