Download or read book Sequence Evolution Function written by Eugene V. Koonin and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.

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 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 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:

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.

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

Download or read book Protein Families written by Christine A. Orengo and published by John Wiley & Sons. This book was released on 2014-02-03 with total page 566 pages. Available in PDF, EPUB and Kindle. Book excerpt: New insights into the evolution and nature of proteins Exploring several distinct approaches, this book describes the methods for comparing protein sequences and protein structures in order to identify homologous relationships and classify proteins and protein domains into evolutionary families. Readers will discover the common features as well as the key philosophical differences underlying the major protein classification systems, including Pfam, Panther, SCOP, and CATH. Moreover, they'll discover how these systems can be used to understand the evolution of protein families as well as understand and predict the degree to which structural and functional information are shared between relatives in a protein family. Edited and authored by leading international experts, Protein Families offers new insights into protein families that are important to medical research as well as protein families that help us understand biological systems and key biological processes such as cell signaling and the immune response. The book is divided into three sections: Section I: Concepts Underlying Protein Family Classification reviews the major strategies for identifying homologous proteins and classifying them into families. Section II: In-Depth Reviews of Protein Families focuses on some fascinating super protein families for which we have substantial amounts of sequence, structural and functional data, making it possible to trace the emergence of functionally diverse relatives. Section III: Review of Protein Families in Important Biological Systems examines protein families associated with a particular biological theme, such as the cytoskeleton. All chapters are extensively illustrated, including depictions of evolutionary relationships. References at the end of each chapter guide readers to original research papers and reviews in the field. Covering protein family classification systems alongside detailed descriptions of select protein families, this book offers biochemists, molecular biologists, protein scientists, structural biologists, and bioinformaticians new insight into the evolution and nature of proteins.

Download or read book Bioinformatics in Rice Research written by Manoj Kumar Gupta and published by Springer Nature. This book was released on 2021-09-24 with total page 609 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an up-to-date review of classic and advanced bioinformatics approaches and their utility in rice research. It summarizes databases and tools for analyzing DNA, proteins and gene expression profiles, mapping genetic variations, annotation of protein and RNA molecules, phylogenetic analysis, and pathway enrichment. In addition, it presents high-throughput technologies that are widely used to provide deep insights into the genetic architecture of important traits in the rice genome. The book subsequently discusses techniques for identifying RNA-protein, DNA-protein interactions, and molecular markers, including SNP and microsatellites, in the contexts of rice breeding and genetics. Lastly, it explores various tools that are used to identify and characterize non-coding RNA in rice and their potential role in rice research.

Download or read book Genetic Databases written by and published by Academic Press. This book was released on 1999-09-01 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computer access is the only way to retrieve up-to-date sequences and this book shows researchers puzzled by the maze of URLs, sites, and searches how to use internet technology to find and analyze genetic data. The book describes the different types of databases, how to use a specific database to find a sequence that you need, and how to analyze the data to compare it with your own work. The content also covers sequence phenotype, mutation, and genetic linkage databases; simple repetitive DNA sequences; gene feature identification; and prediction of structure and function of proteins from sequence information. This book will be invaluable to those starting a career in life sciences research as well as to established researchers wishing to make full use of available resources. - Describes a wide range of databases: DNA, RNA, protein, pathways, and gene expression - Enables readers to access the information they need from databases on the web - Includes a directory of URLs for easy reference - Invaluable for those starting a career in life sciences research and also for established researchers wishing to make full use of available resources

Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

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 Sequence Comparison in Historical Linguistics written by Mattis List and published by Walter de Gruyter GmbH & Co KG. This book was released on 2014-07-21 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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. Dissertations in Language and Cognition This series explores issues of mental representation, lingustic structure and representation, and their interplay. The research presented in this series is grounded in the idea explored in the Collaborative Research Center 'The structure of representations in language, cognition and science' (SFB 991) that there is a universal format for the representation of linguistic and cognitive concepts.

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.

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 Algorithms on Strings Trees and Sequences written by Dan Gusfield and published by Cambridge University Press. This book was released on 1997-05-28 with total page 556 pages. Available in PDF, EPUB and Kindle. Book excerpt: String algorithms are a traditional area of study in computer science. In recent years their importance has grown dramatically with the huge increase of electronically stored text and of molecular sequence data (DNA or protein sequences) produced by various genome projects. This book is a general text on computer algorithms for string processing. In addition to pure computer science, the book contains extensive discussions on biological problems that are cast as string problems, and on methods developed to solve them. It emphasises the fundamental ideas and techniques central to today's applications. New approaches to this complex material simplify methods that up to now have been for the specialist alone. With over 400 exercises to reinforce the material and develop additional topics, the book is suitable as a text for graduate or advanced undergraduate students in computer science, computational biology, or bio-informatics. Its discussion of current algorithms and techniques also makes it a reference for professionals.

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 Of Urfs And Orfs written by Russell F. Doolittle and published by University Science Books. This book was released on 1986 with total page 118 pages. Available in PDF, EPUB and Kindle. Book excerpt: In these days of facile cloning and rapid DNA sequencing, it is not uncommon for investigators to find themselves with a DNA sequence that may or may not code for a known gene product. The sequence is 'open' when read in an appropriate frame, which is to say that there is a long run of amino acid codons before the appearance of a terminator codon. How can we find out if this 'unidentified reading frame' (URF) really codes for a genuine protein, and how can we identify it if it exists? There are two general strategies, both of which can also be applied to the characterization of any 'open reading frame' (ORF), whether or not it has been 'identified'. The first and simplest approach involves computer searching and analysis; the second employs antibodies raised against synthetic peptides patterned on the sequence of the expected gene product. Both methods have been used with great success by many investigators. Each has, nonetheless, its pitfalls and frustrations. This primer is meant to guide the researcher past those obstacles as much as possible. Graduate students and researchers interested in amino acid sequencing; molecular biologists, biochemists, chemists, and biotechnologists.