Download or read book Identification and Application of Repetitive Biological Sequences written by Xuehui Li and published by . This book was released on 2007 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: ABSTRACT: Biological sequences are rich in repeats. For example, more than 50% of the human genome consists of repeats and approximately one-quarter of the amino acids are in repeats. Repeats are subsequences of biased composition. They vary in size from less than a hundred bases to tens of kilobases. They are found as either tandem arrays or dispersed throughout the genome. Repeats can generate insertions, deletions, and unequal crossing-over within genomes and affect protein functions. Hence, repeats play important roles in genome evolution. Repeat identification is normally the first step of studying repeats and a critical part of sequence analysis. For protein sequences, some repeats are popularly referred as low complexity regions (LCRs). Although some computational tools have been developed to identify genomic repeats or LCRs, they all are geared toward specific situations and suffer from different problems. We develop novel methods to identify genomic repeats and LCRs, respectively. Genomic repeats and LCRs present difficulties in genome annotation and analyses. Local alignments between repeats cause many false positives to sequence similarity search. These false positives can cause misassembly of genome sequences or misidentification of repeats as gene/protein sequences. Existing sequence similarity search algorithms either ignore the existence of these repeats or completely remove them. The first strategy produces false positives. The second strategy is not desirable, since no LCR-identification tool is 100% accurate. We develop new algorithms that use LCR information wisely to improve the accuracy and efficiency of sequence search.
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 Repetitive Structures in Biological Sequences Algorithms and Applications written by Marco Pellegrini and published by Frontiers Media SA. This book was released on 2016-10-27 with total page 95 pages. Available in PDF, EPUB and Kindle. Book excerpt: Repetitive structures in biological sequences are emerging as an active focus of research and the unifying concept of "repeatome" (the ensemble of knowledge associated with repeating structures in genomic/proteomic sequences) has been recently proposed in order to highlight several converging trends. One main trend is the ongoing discovery that genomic repetitions are linked to many biological significant events and functions. Diseases (e.g. Huntington's disease) have been causally linked with abnormal expansion of certain repeating sequences in the human genome. Deletions or multiple copy duplications of genes (Copy Number Variations) are important in the aetiology of cancer, Alzheimer, and Parkinson diseases. A second converging trend has been the emergence of many different models and algorithms for detecting non-obvious repeating patterns in strings with applications to in genomic data. Borrowing methodologies from combinatorial pattern, matching, string algorithms, data structures, data mining and machine learning these new approaches break the limitations of the current approaches and offer a new way to design better trans-disciplinary research. The articles collected in this book provides a glance into the rich emerging area of repeatome research, addressing some of its pressing challenges. We believe that these contributions are valuable resources for repeatome research and will stimulate further research from bioinformatic, statistical, and biological points of view.
Download or read book Efficient Algorithms for Identification and Analysis of Repetitive Patterns in Biological Sequences written by Jie Zheng and published by . This book was released on 2006 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Introduction to Computational Biology written by Michael S. Waterman and published by CRC Press. This book was released on 2018-05-02 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biology is in the midst of a era yielding many significant discoveries and promising many more. Unique to this era is the exponential growth in the size of information-packed databases. Inspired by a pressing need to analyze that data, Introduction to Computational Biology explores a new area of expertise that emerged from this fertile field- the combination of biological and information sciences. This introduction describes the mathematical structure of biological data, especially from sequences and chromosomes. After a brief survey of molecular biology, it studies restriction maps of DNA, rough landmark maps of the underlying sequences, and clones and clone maps. It examines problems associated with reading DNA sequences and comparing sequences to finding common patterns. The author then considers that statistics of pattern counts in sequences, RNA secondary structure, and the inference of evolutionary history of related sequences. Introduction to Computational Biology exposes the reader to the fascinating structure of biological data and explains how to treat related combinatorial and statistical problems. Written to describe mathematical formulation and development, this book helps set the stage for even more, truly interdisciplinary work in biology.
Download or read book Repetitive DNA Sequences written by Andrew G. Clark and published by MDPI. This book was released on 2020-03-05 with total page 206 pages. Available in PDF, EPUB and Kindle. Book excerpt: Repetitive DNA is ubiquitous in eukaryotic genomes, and, in many species, comprises the bulk of the genome. Repeats include transposable elements that can self-mobilize and disperse around the genome, and tandemly-repeated satellite DNAs that increase in copy number due to replication slippage and unequal crossing over. Despite their abundance, repetitive DNA is often ignored in genomic studies due to technical challenges in their identification, assembly, and quantification. New technologies and methods are now providing the unprecedented power to analyze repetitive DNAs across diverse taxa. Repetitive DNA is of particular interest because it can represent distinct modes of genome evolution. Some repetitive DNA forms essential genome structures, such as telomeres and centromeres, which are required for proper chromosome maintenance and segregation, whereas others form piRNA clusters that regulate transposable elements; thus, these elements are expected to evolve under purifying selection. In contrast, other repeats evolve selfishly and produce genetic conflicts with their host species that drive adaptive evolution of host defense systems. However, the majority of repeats likely accumulate in eukaryotes in the absence of selection due to mechanisms of transposition and unequal crossing over. Even these neutral repeats may indirectly influence genome evolution as they reach high abundance. In this Special Issue, the contributing authors explore these questions from a range of perspectives.
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 Identification of Transcribed Sequences written by K. Gardiner and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 299 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Human Genome Project, an endeavor to map and sequence the entire human genome, has been in existence for almost seven years. One result of this effort has been the development of increasingly detailed genetic and physical maps spanning large regions of virtually every chromosome. Paralleling this has been the increasingly high resolution mapping of many &wnetic diseases. Together, these developments have facilitated the isolation of specific disease genes and are now motivating the construction of comprehensive transcriptional maps. This latter endeavor represents a new facet of the genome project, and as such requires the recognition and solution of a new set of problems, with the attendant development and application of a new set of techniques. The First International Workshop on the Identification of Transcribed Sequences in the Human Genome was held in 1991 and was attended by 23 investigators. Discussions at this meeting were largely devoted to defining the magnitude of the problem and describing the available techniques. A small number of laboratories reported the development of new techniques (at that time, for example, exon trapping, cDNA hybrid selection, direct cDNA screening, use of splice junction conserved sequences,etc.), but data were too limited to permit comparisons of their relative efficiencies.
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 Repetitive DNA Sequences written by Andrew G. Clark and published by . This book was released on 2020 with total page 206 pages. Available in PDF, EPUB and Kindle. Book excerpt: Repetitive DNA is ubiquitous in eukaryotic genomes, and, in many species, comprises the bulk of the genome. Repeats include transposable elements that can self-mobilize and disperse around the genome, and tandemly-repeated satellite DNAs that increase in copy number due to replication slippage and unequal crossing over. Despite their abundance, repetitive DNA is often ignored in genomic studies due to technical challenges in their identification, assembly, and quantification. New technologies and methods are now providing the unprecedented power to analyze repetitive DNAs across diverse taxa. Repetitive DNA is of particular interest because it can represent distinct modes of genome evolution. Some repetitive DNA forms essential genome structures, such as telomeres and centromeres, which are required for proper chromosome maintenance and segregation, whereas others form piRNA clusters that regulate transposable elements; thus, these elements are expected to evolve under purifying selection. In contrast, other repeats evolve selfishly and produce genetic conflicts with their host species that drive adaptive evolution of host defense systems. However, the majority of repeats likely accumulate in eukaryotes in the absence of selection due to mechanisms of transposition and unequal crossing over. Even these neutral repeats may indirectly influence genome evolution as they reach high abundance. In this Special Issue, the contributing authors explore these questions from a range of perspectives.
Download or read book Computational Molecular Biology written by S. Istrail and published by Gulf Professional Publishing. This book was released on 2003-04-02 with total page 196 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains papers demonstrating the variety and richness of computational problems motivated by molecular biology. The application areas within biology that give rise to the problems studied in these papers include solid molecular modeling, sequence comparison, phylogeny, evolution, mapping, DNA chips, protein folding and 2D gel technology. The mathematical techniques used are algorithmics, combinatorics, optimization, probability, graph theory, complexity and applied mathematics. This is the fourth volume in the Discrete Applied Mathematics series on computational molecular biology, which is devoted to combinatorial and algorithmic techniques in computational molecular biology. This series publishes novel research results on the mathematical and algorithmic foundations of the inherently discrete aspects of computational biology. Key features: . protein folding . phylogenetic inference . 2-dimensional gel analysis . graphical models for sequencing by hybridisation . dynamic visualization of molecular surfaces . problems and algorithms in sequence alignment This book is a reprint of Discrete Applied Mathematics Volume 127, Number 1.
Download or read book Bacterial Genomes written by F.J. de Bruijn and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 786 pages. Available in PDF, EPUB and Kindle. Book excerpt: A wide range of microbiologists, molecular biologists, and molecular evolutionary biologists will find this new volume of singular interest. It summarizes the present knowledge about the structure and stability of microbial genomes, and reviews the techniques used to analyze and fingerprint them. Maps of approximately thirty important microbes, along with articles on the construction and relevant features of the maps are included. The volume is not intended as a complete compendium of all information on microbial genomes, but rather focuses on approaches, methods and good examples of the analysis of small genomes.
Download or read book DNA Structure and Function written by Richard R. Sinden and published by Elsevier. This book was released on 2012-12-02 with total page 423 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA Structure and Function, a timely and comprehensive resource, is intended for any student or scientist interested in DNA structure and its biological implications. The book provides a simple yet comprehensive introduction to nearly all aspects of DNA structure. It also explains current ideas on the biological significance of classic and alternative DNA conformations. Suitable for graduate courses on DNA structure and nucleic acids, the text is also excellent supplemental reading for courses in general biochemistry, molecular biology, and genetics. Explains basic DNA Structure and function clearly and simply Contains up-to-date coverage of cruciforms, Z-DNA, triplex DNA, and other DNA conformations Discusses DNA-protein interactions, chromosomal organization, and biological implications of structure Highlights key experiments and ideas within boxed sections Illustrated with 150 diagrams and figures that convey structural and experimental concepts
Download or read book Molecular Biology of The Cell written by Bruce Alberts 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 Evolution of Translational Omics written by Institute of Medicine and published by National Academies Press. This book was released on 2012-09-13 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: Technologies collectively called omics enable simultaneous measurement of an enormous number of biomolecules; for example, genomics investigates thousands of DNA sequences, and proteomics examines large numbers of proteins. Scientists are using these technologies to develop innovative tests to detect disease and to predict a patient's likelihood of responding to specific drugs. Following a recent case involving premature use of omics-based tests in cancer clinical trials at Duke University, the NCI requested that the IOM establish a committee to recommend ways to strengthen omics-based test development and evaluation. This report identifies best practices to enhance development, evaluation, and translation of omics-based tests while simultaneously reinforcing steps to ensure that these tests are appropriately assessed for scientific validity before they are used to guide patient treatment in clinical trials.
Download or read book Discovery and Analysis of Mosaic Arrangements in Biological Sequences and Structures written by Degui Zhi and published by . This book was released on 2006 with total page 156 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological molecules are composed of discrete units, called domains. The study of the identity and organization of these domains can reveal the correspondence between individual units in different molecules, and the history of domains themselves, which may guide our understanding of the evolutionary history of individual molecules. Currently, the study of domain organization in protein sequences is a mature field; however, the studies of domain organization in other types of biological sequences and protein structures are still in their infancy. There is currently no general framework and specific tools for the identification of domains or for the discovery of the domain organization. Existing tools do not explicitly define what a domain is. In some cases, existing tools (e.g., multiple sequence alignment tools) ignore domain organizations entirely, or represent only a limited subset of domain organization. As a result, the mosaic structures of biological data are left undetected, and we demonstrate that the prevalence of mosaic arrangements is under-appreciated. This dissertation considers shortcomings of current technologies and develops a generic framework for the discovery and analysis of domain organizations in any types of sequential data. We apply this framework in several biological contexts. First we develop the A-Bruijn Aligner (ABA), which represents a multiple sequence alignment (MSA) as a graph that automatically reveals the domain structures. Second, we develop a repeat domain graph approach that decomposes a repeat family library into repeat domains, which is the first method for the comprehensive identification of repeat domains in large genomes. Third, we extend the A-Bruijn graph approach to an exploration of the mosaic arrangements in protein structures. Finally, we propose a new method for structure comparison based on a simplified representation of protein structures using the local curvatures along their generalized backbones.
Download or read book Genomics Circuits and Pathways in Clinical Neuropsychiatry written by Thomas Lehner and published by Academic Press. This book was released on 2016-06-07 with total page 798 pages. Available in PDF, EPUB and Kindle. Book excerpt: This foundational work comprehensively examines the current state of the genetics, genomics and brain circuitry of psychiatric and neurological disorders. It consolidates discoveries of specific genes and genomic regions associated with these conditions, the genetic and anatomic architecture of these syndromes, and addresses how recent advances in genomics are leading to a reappraisal of the biology underlying clinical neuroscience. In doing so, it critically examines the promise and limitations of these discoveries toward treatment, and to the interdisciplinary nature of understanding brain and behavior. Coverage includes new discoveries regarding autism, epilepsy, intellectual disability, dementias, movement disorders, language impairment, disorders of attention, schizophrenia, and bipolar disorder. Genomics, Circuits, and Pathways in Clinical Neuropsychiatry focuses on key concepts, challenges, findings, and methods in genetics, genomics, molecular pathways, brain circuitry, and related neurobiology of neurologic and psychiatric disorders. Provides interdisciplinary appeal in psychiatry, neurology, neuroscience, and genetics Identifies key concepts, methods, and findings Includes coverage of multiple disorders from autism to schizophrenia Reviews specific genes associated with disorders Discusses the genetic architecture of these syndromes Explains how recent findings are influencing the understanding of biology Clarifies the promise of these findings for future treatment
