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.
Download or read book Multiple Biological Sequence Alignment Scoring Functions Algorithms and Evaluations written by Ken D. Nguyen and published by . This book was released on 2011 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Aligning multiple biological sequences such as protein sequences or DNA/RNA sequences is a fundamental task in bioinformatics and sequence analysis. These alignments may contain invaluable information that scientists need to predict the sequences' structures, determine the evolutionary relationships between them, or discover drug-like compounds that can bind to the sequences. Unfortunately, multiple sequence alignment (MSA) is NP-Complete. In addition, the lack of a reliable scoring method makes it very hard to align the sequences reliably and to evaluate the alignment outcomes. In this dissertation, we have designed a new scoring method for use in multiple sequence alignment. Our scoring method encapsulates stereo-chemical properties of sequence residues and their substitution probabilities into a tree-structure scoring scheme. This new technique provides a reliable scoring scheme with low computational complexity. In addition to the new scoring scheme, we have designed an overlapping sequence clustering algorithm to use in our new three multiple sequence alignment algorithms. One of our alignment algorithms uses a dynamic weighted guidance tree to perform multiple sequence alignment in progressive fashion. The use of dynamic weighted tree allows errors in the early alignment stages to be corrected in the subsequence stages. Other two algorithms utilize sequence knowledge-bases and sequence consistency to produce biological meaningful sequence alignments. To improve the speed of the multiple sequence alignment, we have developed a parallel algorithm that can be deployed on reconfigurable computer models. Analytically, our parallel algorithm is the fastest progressive multiple sequence alignment algorithm.
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.
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.
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 156 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.
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.
Download or read book Evaluation of Scoring Functions for Protein Multiple Sequence Alignment Using Structural Alignments written by Sivan Yogev and published by . This book was released on 2005 with total page 39 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Computational Intelligence Methods for Bioinformatics and Biostatistics written by Francesco Masulli and published by Springer Science & Business Media. This book was released on 2010-08-11 with total page 331 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the thoroughly refereed post-conference proceedings of the Sixth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2009, held in Genova, Italy, in October 2009. The revised 23 full papers presented were carefully reviewed and selected from 57 submissions. The main goal of the CIBB meetings is to provide a forum open to researchers from different disciplines to present and discuss problems concerning computational techniques in tools for bioinformatics, gene expression analysis and new perspectives in bioinformatics together with 4 special sessions on using game-theoretical tools in bioinformatics, combining Bayesian and machine learning approaches in bioinformatics: state of the art and future perspectives, data clustering and bioinformatics (DCB 2009) and on intelligent systems for medical decisions support (ISMDS 2009).
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.
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 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: An Easy-to-Use Research Tool for Algorithm Testing and DevelopmentBefore 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 conc
Download or read book Bioinformatics and Computational Biology written by Basant K. Tiwary and published by Springer Nature. This book was released on 2021-11-23 with total page 239 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook introduces fundamental concepts of bioinformatics and computational biology to the students and researchers in biology, medicine, veterinary science, agriculture, and bioengineering . The respective chapters provide detailed information on biological databases, sequence alignment, molecular evolution, next-generation sequencing, systems biology, and statistical computing using R. The book also presents a case-based discussion on clinical, veterinary, agricultural bioinformatics, and computational bioengineering for application-based learning in the respective fields. Further, it offers readers guidance on reconstructing and analysing biological networks and highlights computational methods used in systems medicine and genome-wide association mapping of diseases. Given its scope, this textbook offers an essential introductory book on bioinformatics and computational biology for undergraduate and graduate students in the life sciences, botany, zoology, physiology, biotechnology, bioinformatics, and genomic science as well as systems biology, bioengineering and the agricultural, and veterinary sciences.
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 356 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.
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.
Download or read book Comparative Gene Finding written by Marina Axelson-Fisk and published by Springer Science & Business Media. This book was released on 2010-01-30 with total page 317 pages. Available in PDF, EPUB and Kindle. Book excerpt: Comparative genomics is a new and emerging ?eld, and with the explosion of ava- able biological sequences the requests for faster, more ef?cient and more robust algorithms to analyze all this data are immense. This book is meant to serve as a self-contained instruction of the state-of-the-art of computational gene ?nding in general and of comparative approaches in particular. It is meant as an overview of the various methods that have been applied in the ?eld, and a quick introduction into how computational gene ?nders are built in general. A beginner to the ?eld could use this book as a guide through to the main points to think about when constructing a gene ?nder, and the main algorithms that are in use. On the other hand, the more experienced gene ?nder should be able to use this book as a reference to different methods and to the main components incorporated in these methods. I have focused on the main uses of the covered methods and avoided much of the technical details and general extensions of the models. In exchange I have tried to supply references to more detailed accounts of the different research areas touched upon. The book, however, makes no claim on being comprehensive.
Download or read book Sound and Music Computing written by Tapio Lokki and published by MDPI. This book was released on 2018-06-26 with total page 621 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a printed edition of the Special Issue "Sound and Music Computing" that was published in Applied Sciences
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.
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.
