Biological Sequence Analysis Using The Seqan C Library

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 : Hannes Hauswedell
Publisher : Springer Nature
ISBN 13 : 3030909905
Total Pages : 350 pages
Book Rating : 4.01/5 ( download)

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Download or read book Sequence Analysis and Modern C++ written by Hannes Hauswedell and published by Springer Nature. This book was released on 2022-03-07 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is a book about software engineering, bioinformatics, the C++ programming language and the SeqAn library. In the broadest sense, it will help the reader create better, faster and more reliable software by deepening their understanding of available tools, language features, techniques and design patterns. Every developer who previously worked with C++ will enjoy the in-depth chapter on important changes in the language from C++11 up to and including C++20. In contrast to many resources on Modern C++ that present new features only in small isolated examples, this book represents a more holistic approach: readers will understand the relevance of new features and how they interact in the context of a large software project and not just within a "toy example". Previous experience in creating software with C++ is highly recommended to fully appreciate these aspects. SeqAn3 is a new, re-designed software library. The conception and implementation process is detailed in this book, including a critical reflection on the previous versions of the library. This is particularly helpful to readers who are about to create a large software project themselves, or who are planning a major overhaul of an existing library or framework. While the focus of the book is clearly on software development and design, it also touches on various organisational and administrative aspects like licensing, dependency management and quality control.

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 : Emmanuel Barillot
Publisher : CRC Press
ISBN 13 : 1439831459
Total Pages : 461 pages
Book Rating : 4.58/5 ( download)

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Download or read book Computational Systems Biology of Cancer written by Emmanuel Barillot and published by CRC Press. This book was released on 2012-08-25 with total page 461 pages. Available in PDF, EPUB and Kindle. Book excerpt: The future of cancer research and the development of new therapeutic strategies rely on our ability to convert biological and clinical questions into mathematical models-integrating our knowledge of tumour progression mechanisms with the tsunami of information brought by high-throughput technologies such as microarrays and next-generation sequencin

Author : Alpan Raval
Publisher : CRC Press
ISBN 13 : 1420010360
Total Pages : 329 pages
Book Rating : 4.67/5 ( download)

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Download or read book Introduction to Biological Networks written by Alpan Raval and published by CRC Press. This book was released on 2016-04-19 with total page 329 pages. Available in PDF, EPUB and Kindle. Book excerpt: The new research area of genomics-inspired network biology lacks an introductory book that enables both physical/computational scientists and biologists to obtain a general yet sufficiently rigorous perspective of current thinking. Filling this gap, Introduction to Biological Networks provides a thorough introduction to genomics-inspired network bi

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 : Ken Nguyen
Publisher : John Wiley & Sons
ISBN 13 : 1119272459
Total Pages : 256 pages
Book Rating : 4.58/5 ( 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 2016-06-10 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 : Tieng K. Yap
Publisher : Springer Science & Business Media
ISBN 13 : 1461313910
Total Pages : 219 pages
Book Rating : 4.15/5 ( download)

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Download or read book High Performance Computational Methods for Biological Sequence Analysis written by Tieng K. Yap and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 219 pages. Available in PDF, EPUB and Kindle. Book excerpt: High Performance Computational Methods for Biological Sequence Analysis presents biological sequence analysis using an interdisciplinary approach that integrates biological, mathematical and computational concepts. These concepts are presented so that computer scientists and biomedical scientists can obtain the necessary background for developing better algorithms and applying parallel computational methods. This book will enable both groups to develop the depth of knowledge needed to work in this interdisciplinary field. This work focuses on high performance computational approaches that are used to perform computationally intensive biological sequence analysis tasks: pairwise sequence comparison, multiple sequence alignment, and sequence similarity searching in large databases. These computational methods are becoming increasingly important to the molecular biology community allowing researchers to explore the increasingly large amounts of sequence data generated by the Human Genome Project and other related biological projects. The approaches presented by the authors are state-of-the-art and show how to reduce analysis times significantly, sometimes from days to minutes. High Performance Computational Methods for Biological Sequence Analysis is tremendously important to biomedical science students and researchers who are interested in applying sequence analyses to their studies, and to computational science students and researchers who are interested in applying new computational approaches to biological sequence analyses.

Author : Sorin Draghici
Publisher : CRC Press
ISBN 13 : 1439809763
Total Pages : 1036 pages
Book Rating : 4.61/5 ( download)

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Download or read book Statistics and Data Analysis for Microarrays Using R and Bioconductor written by Sorin Draghici and published by CRC Press. This book was released on 2016-04-19 with total page 1036 pages. Available in PDF, EPUB and Kindle. Book excerpt: Richly illustrated in color, Statistics and Data Analysis for Microarrays Using R and Bioconductor, Second Edition provides a clear and rigorous description of powerful analysis techniques and algorithms for mining and interpreting biological information. Omitting tedious details, heavy formalisms, and cryptic notations, the text takes a hands-on,

Author : Thomas S. Deisboeck
Publisher : CRC Press
ISBN 13 : 9781439814420
Total Pages : 484 pages
Book Rating : 4.22/5 ( download)

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Download or read book Multiscale Cancer Modeling written by Thomas S. Deisboeck and published by CRC Press. This book was released on 2010-12-08 with total page 484 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cancer is a complex disease process that spans multiple scales in space and time. Driven by cutting-edge mathematical and computational techniques, in silico biology provides powerful tools to investigate the mechanistic relationships of genes, cells, and tissues. It enables the creation of experimentally testable hypotheses, the integration of data across scales, and the prediction of tumor progression and treatment outcome (in silico oncology). Drawing on an interdisciplinary group of distinguished international experts, Multiscale Cancer Modeling discusses the scientific and technical expertise necessary to conduct innovative cancer modeling research across scales. It presents contributions from some of the top in silico modeling groups in the United States and Europe. The ultimate goal of multiscale modeling and simulation approaches is their use in clinical practice, such as supporting patient-specific treatment optimization. This volume covers state-of-the-art methods of multiscale cancer modeling and addresses the field’s potential as well as future challenges. It encourages collaborations among researchers in various disciplines to achieve breakthroughs in cancer modeling.