Problems And Solutions In Biological Sequence Analysis

Author : Mark Borodovsky
Publisher : Cambridge University Press
ISBN 13 : 1139458124
Total Pages : 15 pages
Book Rating : 4.22/5 ( download)

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Download or read book Problems and Solutions in Biological Sequence Analysis written by Mark Borodovsky and published by Cambridge University Press. This book was released on 2006-09-04 with total page 15 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is the first of its kind to provide a large collection of bioinformatics problems with accompanying solutions. Notably, the problem set includes all of the problems offered in Biological Sequence Analysis, by Durbin et al. (Cambridge, 1998), widely adopted as a required text for bioinformatics courses at leading universities worldwide. Although many of the problems included in Biological Sequence Analysis as exercises for its readers have been repeatedly used for homework and tests, no detailed solutions for the problems were available. Bioinformatics instructors had therefore frequently expressed a need for fully worked solutions and a larger set of problems for use on courses. This book provides just that: following the same structure as Biological Sequence Analysis and significantly extending the set of workable problems, it will facilitate a better understanding of the contents of the chapters in BSA and will help its readers develop problem-solving skills that are vitally important for conducting successful research in the growing field of bioinformatics. All of the material has been class-tested by the authors at Georgia Tech, where the first ever MSc degree program in Bioinformatics was held.

Author : Richard Durbin
Publisher :
ISBN 13 : 9780511337086
Total Pages : 0 pages
Book Rating : 4.86/5 ( download)

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Download or read book Biological Sequence Analysis written by Richard Durbin and published by . This book was released on 1998 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents up-to-date computer methods for analysing DNA, RNA and protein sequences.

Author : Michael S. Waterman
Publisher : CRC Press
ISBN 13 : 1351437089
Total Pages : 248 pages
Book Rating : 4.80/5 ( download)

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Download or read book Introduction to Computational Biology written by Michael S. Waterman and published by CRC Press. This book was released on 2018-05-02 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biology is in the midst of a era yielding many significant discoveries and promising many more. Unique to this era is the exponential growth in the size of information-packed databases. Inspired by a pressing need to analyze that data, Introduction to Computational Biology explores a new area of expertise that emerged from this fertile field- the combination of biological and information sciences. This introduction describes the mathematical structure of biological data, especially from sequences and chromosomes. After a brief survey of molecular biology, it studies restriction maps of DNA, rough landmark maps of the underlying sequences, and clones and clone maps. It examines problems associated with reading DNA sequences and comparing sequences to finding common patterns. The author then considers that statistics of pattern counts in sequences, RNA secondary structure, and the inference of evolutionary history of related sequences. Introduction to Computational Biology exposes the reader to the fascinating structure of biological data and explains how to treat related combinatorial and statistical problems. Written to describe mathematical formulation and development, this book helps set the stage for even more, truly interdisciplinary work in biology.

Author : Richard Durbin
Publisher : Cambridge University Press
ISBN 13 : 9780521629713
Total Pages : 372 pages
Book Rating : 4.13/5 ( download)

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Download or read book Biological Sequence Analysis written by Richard Durbin and published by Cambridge University Press. This book was released on 1998-04-23 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents up-to-date computer methods for analysing DNA, RNA and protein sequences.

Author : Ken Nguyen
Publisher : John Wiley & Sons
ISBN 13 : 1118229045
Total Pages : 256 pages
Book Rating : 4.40/5 ( download)

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Download or read book Multiple Biological Sequence Alignment written by Ken Nguyen and published by John Wiley & Sons. This book was released on 2016-07-18 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt: Covers the fundamentals and techniques of multiple biological sequence alignment and analysis, and shows readers how to choose the appropriate sequence analysis tools for their tasks This book describes the traditional and modern approaches in biological sequence alignment and homology search. This book contains 11 chapters, with Chapter 1 providing basic information on biological sequences. Next, Chapter 2 contains fundamentals in pair-wise sequence alignment, while Chapters 3 and 4 examine popular existing quantitative models and practical clustering techniques that have been used in multiple sequence alignment. Chapter 5 describes, characterizes and relates many multiple sequence alignment models. Chapter 6 describes how traditionally phylogenetic trees have been constructed, and available sequence knowledge bases can be used to improve the accuracy of reconstructing phylogeny trees. Chapter 7 covers the latest methods developed to improve the run-time efficiency of multiple sequence alignment. Next, Chapter 8 covers several popular existing multiple sequence alignment server and services, and Chapter 9 examines several multiple sequence alignment techniques that have been developed to handle short sequences (reads) produced by the Next Generation Sequencing technique (NSG). Chapter 10 describes a Bioinformatics application using multiple sequence alignment of short reads or whole genomes as input. Lastly, Chapter 11 provides a review of RNA and protein secondary structure prediction using the evolution information inferred from multiple sequence alignments. • Covers the full spectrum of the field, from alignment algorithms to scoring methods, practical techniques, and alignment tools and their evaluations • Describes theories and developments of scoring functions and scoring matrices •Examines phylogeny estimation and large-scale homology search Multiple Biological Sequence Alignment: Scoring Functions, Algorithms and Applications is a reference for researchers, engineers, graduate and post-graduate students in bioinformatics, and system biology and molecular biologists. Ken Nguyen, PhD, is an associate professor at Clayton State University, GA, USA. He received his PhD, MSc and BSc degrees in computer science all from Georgia State University. His research interests are in databases, parallel and distribute computing and bioinformatics. He was a Molecular Basis of Disease fellow at Georgia State and is the recipient of the highest graduate honor at Georgia State, the William M. Suttles Graduate Fellowship. Xuan Guo, PhD, is a postdoctoral associate at Oak Ridge National Lab, USA. He received his PhD degree in computer science from Georgia State University in 2015. His research interests are in bioinformatics, machine leaning, and cloud computing. He is an editorial assistant of International Journal of Bioinformatics Research and Applications. Yi Pan, PhD, is a Regents' Professor of Computer Science and an Interim Associate Dean and Chair of Biology at Georgia State University. He received his BE and ME in computer engineering from Tsinghua University in China and his PhD in computer science from the University of Pittsburgh. Dr. Pan's research interests include parallel and distributed computing, optical networks, wireless networks and bioinformatics. He has published more than 180 journal papers with about 60 papers published in various IEEE/ACM journals. He is co-editor along with Albert Y. Zomaya of the Wiley Series in Bioinformatics.

Author : Veli Mäkinen
Publisher : Cambridge University Press
ISBN 13 : 1009341219
Total Pages : 470 pages
Book Rating : 4.19/5 ( download)

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Download or read book Genome-Scale Algorithm Design written by Veli Mäkinen and published by Cambridge University Press. This book was released on 2023-10-12 with total page 470 pages. Available in PDF, EPUB and Kindle. Book excerpt: Guided by standard bioscience workflows in high-throughput sequencing analysis, this book for graduate students, researchers, and professionals in bioinformatics and computer science offers a unified presentation of genome-scale algorithms. This new edition covers the use of minimizers and other advanced data structures in pangenomics approaches.

Author : Andreas Gogol-Döring
Publisher : CRC Press
ISBN 13 : 9781420076240
Total Pages : 329 pages
Book Rating : 4.48/5 ( download)

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Download or read book Biological Sequence Analysis Using the SeqAn C++ Library written by Andreas Gogol-Döring and published by CRC Press. This book was released on 2009-11-11 with total page 329 pages. Available in PDF, EPUB and Kindle. Book excerpt: An Easy-to-Use Research Tool for Algorithm Testing and Development Before the SeqAn project, there was clearly a lack of available implementations in sequence analysis, even for standard tasks. Implementations of needed algorithmic components were either unavailable or hard to access in third-party monolithic software products. Addressing these concerns, the developers of SeqAn created a comprehensive, easy-to-use, open source C++ library of efficient algorithms and data structures for the analysis of biological sequences. Written by the founders of this project, Biological Sequence Analysis Using the SeqAn C++ Library covers the SeqAn library, its documentation, and the supporting infrastructure. The first part of the book describes the general library design. It introduces biological sequence analysis problems, discusses the benefit of using software libraries, summarizes the design principles and goals of SeqAn, details the main programming techniques used in SeqAn, and demonstrates the application of these techniques in various examples. Focusing on the components provided by SeqAn, the second part explores basic functionality, sequence data structures, alignments, pattern and motif searching, string indices, and graphs. The last part illustrates applications of SeqAn to genome alignment, consensus sequence in assembly projects, suffix array construction, and more. This handy book describes a user-friendly library of efficient data types and algorithms for sequence analysis in computational biology. SeqAn enables not only the implementation of new algorithms, but also the sound analysis and comparison of existing algorithms. Visit SeqAn for more information.

Author : Richard Durbin
Publisher : Cambridge University Press
ISBN 13 : 113945739X
Total Pages : 332 pages
Book Rating : 4.92/5 ( download)

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Download or read book Biological Sequence Analysis written by Richard Durbin and published by Cambridge University Press. This book was released on 1998-04-23 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.

Author : S.L. Salzberg
Publisher : Elsevier
ISBN 13 : 9780080860930
Total Pages : 368 pages
Book Rating : 4.31/5 ( download)

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Download or read book Computational Methods in Molecular Biology written by S.L. Salzberg and published by Elsevier. This book was released on 1998-06-19 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational biology is a rapidly expanding field, and the number and variety of computational methods used for DNA and protein sequence analysis is growing every day. These algorithms are extremely valuable to biotechnology companies and to researchers and teachers in universities. This book explains the latest computer technology for analyzing DNA, RNA, and protein sequences. Clear and easy to follow, designed specifically for the non-computer scientist, it will help biologists make better choices on which algorithm to use. New techniques and demonstrations are elucidated, as are state-of-the-art problems, and more advanced material on the latest algorithms. The primary audience for this volume are molecular biologists working either in biotechnology companies or academic research environments, individual researchers and the institutions they work for, and students. Any biologist who relies on computers should want this book. A secondary audience will be computer scientists developing techniques with applications in biology. An excellent reference for leading techniques, it will also help introduce computer scientists to the biology problems. This is an outstanding work which will be ideal for the increasing number of scientists moving into computational biology.

Author : Robert M. Miura
Publisher : American Mathematical Soc.
ISBN 13 : 9780821897119
Total Pages : 142 pages
Book Rating : 4.1X/5 ( download)

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Download or read book Some Mathematical Questions in Biology written by Robert M. Miura and published by American Mathematical Soc.. This book was released on 1986-12-31 with total page 142 pages. Available in PDF, EPUB and Kindle. Book excerpt: Several data banks around the world are accumulating DNA sequences at a feverish rate, with tremendous potential for furthering our knowledge of how biological systems code and pass on information. The sophisticated mathematical analysis of that data is just beginning. The Eighteenth Annual Symposium on Some Mathematical Questions in Biology was held in conjunction with the Annual Meeting of the AAAS and brought together speakers knowledgeable in both biology and mathematics to discuss these developments and to emphasize the need for rigorous, efficient computational tools. These computational tools include biologically relevant definitions of sequence similarity and string matching algorithms. The solutions for some of these problems have great generality; the string matching methods first developed for biological sequences have now been applied to areas such as geology, linguistics, and speech recognition. There is a great potential here for creating of new mathematics to handle this growing data base, with new applications for many areas of mathematics, computer science, and statistics.