Multiple Biological Sequence Alignment

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Multiple Biological Sequence Alignment

Author : Ken Nguyen
Publisher : John Wiley & Sons
ISBN 13 : 1118229045
Total Pages : 256 pages
Book Rating : 4.1/5 (182 download)

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Book Synopsis Multiple Biological Sequence Alignment by : Ken Nguyen

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.

Biological Sequence Analysis

Author : Richard Durbin
Publisher : Cambridge University Press
ISBN 13 : 113945739X
Total Pages : 372 pages
Book Rating : 4.1/5 (394 download)

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Book Synopsis Biological Sequence Analysis by : Richard Durbin

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: 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.

Multiple Sequence Alignment Methods

Author : David J Russell
Publisher : Humana
ISBN 13 : 9781493960477
Total Pages : 0 pages
Book Rating : 4.9/5 (64 download)

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Book Synopsis Multiple Sequence Alignment Methods by : David J Russell

Download or read book Multiple Sequence Alignment Methods written by David J Russell and published by Humana. This book was released on 2016-08-23 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Parameter Advising for Multiple Sequence Alignment

Author : Dan DeBlasio
Publisher : Springer
ISBN 13 : 3319649183
Total Pages : 152 pages
Book Rating : 4.3/5 (196 download)

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Book Synopsis Parameter Advising for Multiple Sequence Alignment by : Dan DeBlasio

Download or read book Parameter Advising for Multiple Sequence Alignment written by Dan DeBlasio and published by Springer. This book was released on 2018-01-04 with total page 152 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 Alignments

Author : Theodor Sperlea
Publisher : Springer Nature
ISBN 13 : 3662644738
Total Pages : 106 pages
Book Rating : 4.6/5 (626 download)

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Book Synopsis Multiple Sequence Alignments by : Theodor Sperlea

Download or read book Multiple Sequence Alignments written by Theodor Sperlea and published by Springer Nature. This book was released on 2022-02-17 with total page 106 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Essential Bioinformatics

Author : Jin Xiong
Publisher : Cambridge University Press
ISBN 13 : 113945062X
Total Pages : 360 pages
Book Rating : 4.1/5 (394 download)

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Book Synopsis Essential Bioinformatics by : Jin Xiong

Download or read book Essential Bioinformatics written by Jin Xiong and published by Cambridge University Press. This book was released on 2006-03-13 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Author : Michael S. Rosenberg
Publisher : Univ of California Press
ISBN 13 : 0520256972
Total Pages : 357 pages
Book Rating : 4.5/5 (22 download)

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Book Synopsis Sequence Alignment by : Michael S. Rosenberg

Download or read book Sequence Alignment written by Michael S. Rosenberg and published by Univ of California Press. This book was released on 2009 with total page 357 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Multiple Sequence Alignment

Author : Kazutaka Katoh
Publisher : Humana
ISBN 13 : 9781071610350
Total Pages : 0 pages
Book Rating : 4.6/5 (13 download)

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Book Synopsis Multiple Sequence Alignment by : Kazutaka Katoh

Download or read book Multiple Sequence Alignment written by Kazutaka Katoh and published by Humana. This book was released on 2020-12-09 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chapter “Alignment of Biological Sequences with Jalview” is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Sequence Comparison

Author : Kun-Mao Chao
Publisher : Springer Science & Business Media
ISBN 13 : 184800320X
Total Pages : 218 pages
Book Rating : 4.8/5 (48 download)

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Book Synopsis Sequence Comparison by : Kun-Mao Chao

Download or read book Sequence Comparison written by Kun-Mao Chao and published by Springer Science & Business Media. This book was released on 2008-11-27 with total page 218 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Fundamentals of Bioinformatics and Computational Biology

Author : Gautam B. Singh
Publisher : Springer
ISBN 13 : 3319114034
Total Pages : 345 pages
Book Rating : 4.3/5 (191 download)

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Book Synopsis Fundamentals of Bioinformatics and Computational Biology by : Gautam B. Singh

Download or read book Fundamentals of Bioinformatics and Computational Biology written by Gautam B. Singh and published by Springer. This book was released on 2014-09-24 with total page 345 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book offers comprehensive coverage of all the core topics of bioinformatics, and includes practical examples completed using the MATLAB bioinformatics toolboxTM. It is primarily intended as a textbook for engineering and computer science students attending advanced undergraduate and graduate courses in bioinformatics and computational biology. The book develops bioinformatics concepts from the ground up, starting with an introductory chapter on molecular biology and genetics. This chapter will enable physical science students to fully understand and appreciate the ultimate goals of applying the principles of information technology to challenges in biological data management, sequence analysis, and systems biology. The first part of the book also includes a survey of existing biological databases, tools that have become essential in today’s biotechnology research. The second part of the book covers methodologies for retrieving biological information, including fundamental algorithms for sequence comparison, scoring, and determining evolutionary distance. The main focus of the third part is on modeling biological sequences and patterns as Markov chains. It presents key principles for analyzing and searching for sequences of significant motifs and biomarkers. The last part of the book, dedicated to systems biology, covers phylogenetic analysis and evolutionary tree computations, as well as gene expression analysis with microarrays. In brief, the book offers the ideal hands-on reference guide to the field of bioinformatics and computational biology.

Statistics for Bioinformatics

Author : Julie Thompson
Publisher : Elsevier
ISBN 13 : 0081019610
Total Pages : 146 pages
Book Rating : 4.0/5 (81 download)

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Book Synopsis Statistics for Bioinformatics by : Julie Thompson

Download or read book Statistics for Bioinformatics written by Julie Thompson and published by Elsevier. This book was released on 2016-11-24 with total page 146 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Handbook of Discrete and Combinatorial Mathematics

Author : Kenneth H. Rosen
Publisher : CRC Press
ISBN 13 : 135164405X
Total Pages : 1611 pages
Book Rating : 4.3/5 (516 download)

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Book Synopsis Handbook of Discrete and Combinatorial Mathematics by : Kenneth H. Rosen

Download or read book Handbook of Discrete and Combinatorial Mathematics written by Kenneth H. Rosen and published by CRC Press. This book was released on 2017-10-19 with total page 1611 pages. Available in PDF, EPUB and Kindle. Book excerpt: Handbook of Discrete and Combinatorial Mathematics provides a comprehensive reference volume for mathematicians, computer scientists, engineers, as well as students and reference librarians. The material is presented so that key information can be located and used quickly and easily. Each chapter includes a glossary. Individual topics are covered in sections and subsections within chapters, each of which is organized into clearly identifiable parts: definitions, facts, and examples. Examples are provided to illustrate some of the key definitions, facts, and algorithms. Some curious and entertaining facts and puzzles are also included. Readers will also find an extensive collection of biographies. This second edition is a major revision. It includes extensive additions and updates. Since the first edition appeared in 1999, many new discoveries have been made and new areas have grown in importance, which are covered in this edition.

Problems and Solutions in Biological Sequence Analysis

Author : Mark Borodovsky
Publisher : Cambridge University Press
ISBN 13 : 1139458124
Total Pages : 15 pages
Book Rating : 4.1/5 (394 download)

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Book Synopsis Problems and Solutions in Biological Sequence Analysis by : Mark Borodovsky

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.

Bioinformatics for Everyone

Author : Mohammad Yaseen Sofi
Publisher : Academic Press
ISBN 13 : 0323911293
Total Pages : 268 pages
Book Rating : 4.3/5 (239 download)

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Book Synopsis Bioinformatics for Everyone by : Mohammad Yaseen Sofi

Download or read book Bioinformatics for Everyone written by Mohammad Yaseen Sofi and published by Academic Press. This book was released on 2021-09-14 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioinformatics for Everyone provides a brief overview on currently used technologies in the field of bioinformatics—interpreted as the application of information science to biology— including various online and offline bioinformatics tools and softwares. The book presents valuable knowledge in a simplified way to help students and researchers easily apply bioinformatics tools and approaches to their research and lab routines. Several protocols and case studies that can be reproduced by readers to suit their needs are also included. Explains the most relevant bioinformatics tools available in a didactic manner so that readers can easily apply them to their research Includes several protocols that can be used in different types of research work or in lab routines Discusses upcoming technologies and their impact on biological/biomedical sciences

Parallel Computational Fluid Dynamics

Author : Kenli Li
Publisher : Springer
ISBN 13 : 3642539629
Total Pages : 626 pages
Book Rating : 4.6/5 (425 download)

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Book Synopsis Parallel Computational Fluid Dynamics by : Kenli Li

Download or read book Parallel Computational Fluid Dynamics written by Kenli Li and published by Springer. This book was released on 2014-03-08 with total page 626 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 25th International Conference on Parallel Computational Fluid Dynamics, ParCFD 2013, held in Changsha, China, in May 2013. The 35 revised full papers presented were carefully reviewed and selected from more than 240 submissions. The papers address issues such as parallel algorithms, developments in software tools and environments, unstructured adaptive mesh applications, industrial applications, atmospheric and oceanic global simulation, interdisciplinary applications and evaluation of computer architectures and software environments.

Atlas of Protein Sequence and Structure

Author :
Publisher :
ISBN 13 :
Total Pages : 132 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis Atlas of Protein Sequence and Structure by :

Download or read book Atlas of Protein Sequence and Structure written by and published by . This book was released on 1973 with total page 132 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Multiple Sequence Alignment

Author : Kazutaka Katoh
Publisher : Humana
ISBN 13 : 9781071610381
Total Pages : 321 pages
Book Rating : 4.6/5 (13 download)

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Book Synopsis Multiple Sequence Alignment by : Kazutaka Katoh

Download or read book Multiple Sequence Alignment written by Kazutaka Katoh and published by Humana. This book was released on 2020-12-09 with total page 321 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chapter “Alignment of Biological Sequences with Jalview” is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.