Sequence Comparison
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Sequence Comparison
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Author : Kun-Mao Chao
language : en
Publisher: Springer Science & Business Media
Release Date : 2008-11-27
Sequence Comparison written by Kun-Mao Chao and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-11-27 with Computers categories.
Biomolecular sequence comparison is the origin of bioinformatics. This book gives a complete in-depth treatment of the study of sequence comparison. A comprehensive introduction is followed by a focus on alignment algorithms and techniques, proceeded by a discussion of the theory. The book examines alignment methods and techniques, features a new issue of sequence comparison - the spaced seed technique, addresses several new flexible strategies for coping with various scoring schemes, and covers the theory on the significance of high-scoring segment pairs between two unalignment sequences. Useful appendices on basic concepts in molecular biology, primer in statistics and software for sequence alignment are included in this reader-friendly text, as well as chapter-ending exercise and research questions A state-of-the-art study of sequence alignment and homology search, this is an ideal reference for advanced students studying bioinformatics and will appeal to biologists who wish to know how to use homology search tools.
Sequence Comparison In Historical Linguistics
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Author : Mattis List
language : en
Publisher: Walter de Gruyter GmbH & Co KG
Release Date : 2014-07-21
Sequence Comparison In Historical Linguistics written by Mattis List and has been published by Walter de Gruyter GmbH & Co KG this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-07-21 with Language Arts & Disciplines categories.
The comparison of sound sequences (words, morphemes) constitutes the core of many techniques and methods in historical linguistics. With the help of these techniques, corresponding sounds can be determined, historically related words can be identified, and the history of languages can be uncovered. So far, the application of traditional techniques for sequence comparison is very tedious and time-consuming, since scholars have to apply them manually, without computational support. In this study, algorithms from bioinformatics are used to develop computational methods for sequence comparison in historical linguistics. The new methods automatize several steps of the traditional comparative method and can thus help to ease the painstaking work of language comparison.
Essential Bioinformatics
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Author : Jin Xiong
language : en
Publisher: Cambridge University Press
Release Date : 2006-03-13
Essential Bioinformatics written by Jin Xiong and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006-03-13 with Science categories.
Essential Bioinformatics is a concise yet comprehensive textbook of bioinformatics, which provides a broad introduction to the entire field. Written specifically for a life science audience, the basics of bioinformatics are explained, followed by discussions of the state-of-the-art computational tools available to solve biological research problems. All key areas of bioinformatics are covered including biological databases, sequence alignment, genes and promoter prediction, molecular phylogenetics, structural bioinformatics, genomics and proteomics. The book emphasizes how computational methods work and compares the strengths and weaknesses of different methods. This balanced yet easily accessible text will be invaluable to students who do not have sophisticated computational backgrounds. Technical details of computational algorithms are explained with a minimum use of mathematical formulae; graphical illustrations are used in their place to aid understanding. The effective synthesis of existing literature as well as in-depth and up-to-date coverage of all key topics in bioinformatics make this an ideal textbook for all bioinformatics courses taken by life science students and for researchers wishing to develop their knowledge of bioinformatics to facilitate their own research.
Sequence Alignment
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Author : Michael S. Rosenberg Ph. D.
language : en
Publisher: Univ of California Press
Release Date : 2009-03-11
Sequence Alignment written by Michael S. Rosenberg Ph. D. and has been published by Univ of California Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-03-11 with Science categories.
The sequencing of the human genome involved thousands of scientists but used relatively few tools. Today, obtaining sequences is simpler, but aligning the sequences—making sure that sequences from one source are properly compared to those from other sources—remains a complicated but underappreciated aspect of comparative molecular biology. This volume, the first to focus on this crucial step in analyzing sequence data, is about the practice of alignment, the procedures by which alignments are established, and more importantly, how the outcomes of any alignment algorithm should be interpreted. Edited by Michael S. Rosenberg with essays by many of the field's leading experts, Sequence Alignment covers molecular causes, computational advances, approaches for assessing alignment quality, and philosophical underpinnings of the algorithms themselves.
Xquery
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Author : Michael Brundage
language : en
Publisher: Addison-Wesley Professional
Release Date : 2004
Xquery written by Michael Brundage and has been published by Addison-Wesley Professional this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004 with Computers categories.
From corporate IT departments to academic institutions, XML has become the language of choice for storing and transmitting data across diverse application domains. For those new to the XML query language, XQuery, this example-rich text serves as a tutorial that brings readers quickly up to speed on XQuery's data model, type system, and core language features.
Computational Techniques For Biological Sequence Analysis
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Author : Saiyed Umer
language : en
Publisher: CRC Press
Release Date : 2025-06-17
Computational Techniques For Biological Sequence Analysis written by Saiyed Umer and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2025-06-17 with Computers categories.
This book provides an overview of basic and advanced computational techniques for analyzing and understanding protein, RNA, and DNA sequences. It covers effective computing techniques for DNA and protein classifications, evolutionary and sequence information analysis, evolutionary algorithms, and ensemble algorithms. Furthermore, the book reviews the role of machine learning techniques, artificial intelligence, ensemble learning, and sequence-based features in predicting post-translational modifications in proteins, DNA methylation, and mRNA methylation, along with their functional implications. The book also discusses the prediction of protein–protein and protein–DNA interactions, protein structure, and function using computational methods. It also presents techniques for quantitative analysis of protein–DNA interactions and protein methylation and their involvement in gene regulation. Additionally, the use of nature-inspired algorithms to gain insights into gene regulatory mechanisms and metabolic pathways in human diseases is explored. This book acts as a useful reference for bioinformaticians and computational biologists working in the fields of molecular biology, genomics, and bioinformatics. Key Features: Reviews machine learning techniques for DNA sequence classification and protein structure prediction Discusses genetic algorithms for analyzing multiple sequence alignments and predicting protein–protein interaction sites Explores computational methods for quantitative analysis of protein–DNA interactions Examine the role of nature-inspired algorithms in understanding the gene regulation and metabolic pathways Covers evolutionary algorithms and sequence-based features in predicting post-translational modifications
Introduction To Bioinformatics
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Author : Stephen A. Krawetz
language : en
Publisher: Springer Science & Business Media
Release Date : 2003-01-31
Introduction To Bioinformatics written by Stephen A. Krawetz and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2003-01-31 with Science categories.
to Bioinformatics A Theoretical and Practical Approach Edited by Stephen A. Krawetz, PhD Wayne State University School of Medicine, Detroit MI and David D. Womble, PhD Wayne State University School of Medicine, Detroit, MI ~ Springer Science+ ~ Business Media, LLC © 2003 Springer Science+Business Media New York Originally published by Humana Press !ne. in 2003 Softcover reprint of the hardcover 1 st edition 2003 humanapress.com Ali rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise without written permission from the Publisher. Ali papers, comments, opinions, conclusions, or recommendations are those of the author(s), and do not necessarily reflect the views of the publisher. This publication is printed on acid-free paper. G) ANSI Z39.48-1984 (American Standards Institute) Permanence of Paper for Printed Library Materials. Production Editor: Mark J. Breaugh. Cover design by Patricia F. Cleary and Paul A. Thiessen. Cover illustration by Paul A. Thiessen, chemicalgraphics.com.
Advances In Gpu Research And Practice
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Author : Hamid Sarbazi-Azad
language : en
Publisher: Morgan Kaufmann
Release Date : 2016-09-15
Advances In Gpu Research And Practice written by Hamid Sarbazi-Azad and has been published by Morgan Kaufmann this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-09-15 with Computers categories.
Advances in GPU Research and Practice focuses on research and practices in GPU based systems. The topics treated cover a range of issues, ranging from hardware and architectural issues, to high level issues, such as application systems, parallel programming, middleware, and power and energy issues. Divided into six parts, this edited volume provides the latest research on GPU computing. Part I: Architectural Solutions focuses on the architectural topics that improve on performance of GPUs, Part II: System Software discusses OS, compilers, libraries, programming environment, languages, and paradigms that are proposed and analyzed to help and support GPU programmers. Part III: Power and Reliability Issues covers different aspects of energy, power, and reliability concerns in GPUs. Part IV: Performance Analysis illustrates mathematical and analytical techniques to predict different performance metrics in GPUs. Part V: Algorithms presents how to design efficient algorithms and analyze their complexity for GPUs. Part VI: Applications and Related Topics provides use cases and examples of how GPUs are used across many sectors. - Discusses how to maximize power and obtain peak reliability when designing, building, and using GPUs - Covers system software (OS, compilers), programming environments, languages, and paradigms proposed to help and support GPU programmers - Explains how to use mathematical and analytical techniques to predict different performance metrics in GPUs - Illustrates the design of efficient GPU algorithms in areas such as bioinformatics, complex systems, social networks, and cryptography - Provides applications and use case scenarios in several different verticals, including medicine, social sciences, image processing, and telecommunications
Sequence Analysis Primer
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Author : Michael Gribskov
language : en
Publisher: Oxford University Press
Release Date : 1993-09-23
Sequence Analysis Primer written by Michael Gribskov and has been published by Oxford University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 1993-09-23 with Science categories.
Computerized sequence analysis is an integral part of biotechnological research, yet many biologists have received no formal training in this important technology. Sequence Analysis Primer offers the beginner the necessary background to enter this vital field and helps more seasoned researchers to fine-tune their approach. It covers basic data manipulation such as homology searches, stem-loop identification, and protein secondary structure prediction, and is compatible with most sequence analysis programs. A detailed example giving steps for characterizing a new gene sequence provides users with hands-on experience when combined with their current software. The book will be invaluable to researchers and students in molecular biology, genetics, biochemistry, microbiology, and biotechnology.
Multiple Biological Sequence Alignment
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Author : Ken Nguyen
language : en
Publisher: John Wiley & Sons
Release Date : 2016-07-18
Multiple Biological Sequence Alignment written by Ken Nguyen and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-07-18 with Computers categories.
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.