Multiple Sequence Alignments
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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.
Multiple Sequence Alignments
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Author : Theodor Sperlea
language : en
Publisher: Springer Nature
Release Date : 2022-02-17
Multiple Sequence Alignments written by Theodor Sperlea and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-02-17 with Science categories.
This book is a practical guide for biologists who use multiple sequence alignments (MSAs) for their data analysis and are looking for a comprehensive overview of the many different programs. Despite their important role in data analysis, there is uncertainty among researchers about exactly how MSA programs work - not to mention how and why the different analyzes lead to different results. Which program is the right one for evaluating my data and how can I ensure that I have drawn all relevant findings from the alignments? This book offers helpful explanations and background information without requiring extensive bioinformatics knowledge and slowly introduces the reader to the topic.In the first part of the book, the possible fields of application as well as the formats that are usually produced by MSA programs are described in detail. The central algorithms as well as the internal processes of the most common MSA programs of the past and the present are also explained in an uncomplicated manner in greater detail. The second part of the book is a detailed, data-based comparison between MSA programs, which is intended to help you decide which program to use for your next alignment.
Multiple Sequence Alignment Methods
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Author : David J Russell
language : en
Publisher: Humana
Release Date : 2016-08-23
Multiple Sequence Alignment Methods written by David J Russell and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-08-23 with Science categories.
From basic performing of sequence alignment through a proficiency at understanding how most industry-standard alignment algorithms achieve their results, Multiple Sequence Alignment Methods describes numerous algorithms and their nuances in chapters written by the experts who developed these algorithms. The various multiple sequence alignment algorithms presented in this handbook give a flavor of the broad range of choices available for multiple sequence alignment generation, and their diversity is a clear reflection of the complexity of the multiple sequence alignment problem and the amount of information that can be obtained from multiple sequence alignments. Each of these chapters not only describes the algorithm it covers but also presents instructions and tips on using their implementation, as is fitting with its inclusion in the highly successful Methods in Molecular Biology series. Authoritative and practical, Multiple Sequence Alignment Methods provides a readily available resource which will allow practitioners to experiment with different algorithms and find the particular algorithm that is of most use in their application.
Sequence Alignment
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Author : Michael S. Rosenberg
language : en
Publisher: Univ of California Press
Release Date : 2009
Sequence Alignment written by Michael S. Rosenberg 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 with Computers categories.
The sequencing of the human genome involved thousands of scientists but used relatively few tools. Obtaining sequences is simpler, but aligning the sequences remains a complicated but underappreciated aspect of comparative molecular biology. This book discusses the practice of alignment, and the procedures by which alignments are established.
Statistics For Bioinformatics
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Author : Julie Thompson
language : en
Publisher: Elsevier
Release Date : 2016-11-24
Statistics For Bioinformatics written by Julie Thompson and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-11-24 with Medical categories.
Statistics for Bioinformatics: Methods for Multiple Sequence Alignment provides an in-depth introduction to the most widely used methods and software in the bioinformatics field. With the ever increasing flood of sequence information from genome sequencing projects, multiple sequence alignment has become one of the cornerstones of bioinformatics. Multiple sequence alignments are crucial for genome annotation, as well as the subsequent structural, functional, and evolutionary studies of genes and gene products. Consequently, there has been renewed interest in the development of novel multiple sequence alignment algorithms and more efficient programs. Explains the dynamics that animate health systems Explores tracks to build sustainable and equal architecture of health systems Examines the advantages and disadvantages of the different approaches to care integration and the management of health information
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.
Parameter Advising For Multiple Sequence Alignment
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Author : Dan DeBlasio
language : en
Publisher: Springer
Release Date : 2018-01-04
Parameter Advising For Multiple Sequence Alignment written by Dan DeBlasio and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-01-04 with Computers categories.
This book develops a new approach called parameter advising for finding a parameter setting for a sequence aligner that yields a quality alignment of a given set of input sequences. In this framework, a parameter advisor is a procedure that automatically chooses a parameter setting for the input, and has two main ingredients: (a) the set of parameter choices considered by the advisor, and (b) an estimator of alignment accuracy used to rank alignments produced by the aligner. On coupling a parameter advisor with an aligner, once the advisor is trained in a learning phase, the user simply inputs sequences to align, and receives an output alignment from the aligner, where the advisor has automatically selected the parameter setting. The chapters first lay out the foundations of parameter advising, and then cover applications and extensions of advising. The content • examines formulations of parameter advising and their computational complexity, • develops methods for learning good accuracy estimators, • presents approximation algorithms for finding good sets of parameter choices, and • assesses software implementations of advising that perform well on real biological data. Also explored are applications of parameter advising to • adaptive local realignment, where advising is performed on local regions of the sequences to automatically adapt to varying mutation rates, and • ensemble alignment, where advising is applied to an ensemble of aligners to effectively yield a new aligner of higher quality than the individual aligners in the ensemble. The book concludes by offering future directions in advising research.
Multiple Sequence Alignment
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Author : Kazutaka Katoh
language : en
Publisher: Humana
Release Date : 2020-12-09
Multiple Sequence Alignment written by Kazutaka Katoh and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-12-09 with Science categories.
Chapter “Alignment of Biological Sequences with Jalview” is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Partial Order Graphs For Multiple Sequence Alignment
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Author : Catherine S. Grasso
language : en
Publisher:
Release Date : 2005
Partial Order Graphs For Multiple Sequence Alignment written by Catherine S. Grasso and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005 with categories.
Bioinformatics Sequence Alignment And Markov Models
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Author : Kal Renganathan Sharma
language : en
Publisher: McGraw Hill Professional
Release Date : 2008-09-29
Bioinformatics Sequence Alignment And Markov Models written by Kal Renganathan Sharma and has been published by McGraw Hill Professional this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-09-29 with Technology & Engineering categories.
GET FULLY UP-TO-DATE ON BIOINFORMATICS-THE TECHNOLOGY OF THE 21ST CENTURY Bioinformatics showcases the latest developments in the field along with all the foundational information you'll need. It provides in-depth coverage of a wide range of autoimmune disorders and detailed analyses of suffix trees, plus late-breaking advances regarding biochips and genomes. Featuring helpful gene-finding algorithms, Bioinformatics offers key information on sequence alignment, HMMs, HMM applications, protein secondary structure, microarray techniques, and drug discovery and development. Helpful diagrams accompany mathematical equations throughout, and exercises appear at the end of each chapter to facilitate self-evaluation. This thorough, up-to-date resource features: Worked-out problems illustrating concepts and models End-of-chapter exercises for self-evaluation Material based on student feedback Illustrations that clarify difficult math problems A list of bioinformatics-related websites Bioinformatics covers: Sequence representation and alignment Hidden Markov models Applications of HMMs Gene finding Protein secondary structure prediction Microarray techniques Drug discovery and development Internet resources and public domain databases