[PDF] Computational Algorithms For Comparative Genomics eBook

Author : Khalid Mahmood
Publisher :
Page : 222 pages
File Size : 16,77 MB
Release : 2012
Category :
ISBN :

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Advances in high throughput genome sequencing has presented an opportunity to study how species are related, especially, in terms of their evolution and molecular functions. However, the capability to generate genome sequence data outweighs the ability to decipher and translate this data to biological information. Therefore, computational methods play a key role in deciphering large and complex genome data that is essential for bridging the growing gap between genes of known and unknown functions. To this end, computational comparative genomics is an essential task for studying the organization, topology and conservation of genes and strings of genes that lends to a better biological understanding of gene function and annotation. At the core of comparative genomic is the task of identifying gene relationships or matches across genomes. However, large dimensionality of genome data and complex evolutionary artefacts means that gene matching is a non-trivial task and new computational approaches are constantly required to address these issues. This thesis presents new algorithms for gene matching to identify gene relationships across genomes (or complete proteomes). Novel computational methods are presented here that (1) perform comparisons between small related species such as microbial strains, (2) calculate gene matching on large-scale genome data to identify gene orthologs, conserved gene strings and evolutionary rearrangements, (3) calculate complex orthologous relationships such as co-orthologs and (4) calculate rapid large-scale sequence comparisons. The methods described here are applied to a variety of genome comparisons ranging from small microbial strains to large eukarytoes such as human, mouse and rat genomes. The results from these comparisons revealed orthologous and co-orthologous genes, syntenic regions, conserved gene strings and genome rearrangements with high accuracy. Further experiments have also shown the methods described here to be computationally efficient and robust.

Author : Cedric Chauve
Publisher : Springer Science & Business Media
Page : 329 pages
File Size : 30,64 MB
Release : 2013-09-17
Category : Computers
ISBN : 1447152980

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This authoritative text/reference presents a review of the history, current status, and potential future directions of computational biology in molecular evolution. Gathering together the unique insights of an international selection of prestigious researchers, this must-read volume examines the latest developments in the field, the challenges that remain, and the new avenues emerging from the growing influx of sequence data. These viewpoints build upon the pioneering work of David Sankoff, one of the founding fathers of computational biology, and mark the 50th anniversary of his first scientific article. The broad spectrum of rich contributions in this essential collection will appeal to all computer scientists, mathematicians and biologists involved in comparative genomics, phylogenetics and related areas.

Author : Eugene V. Koonin
Publisher : Springer Science & Business Media
Page : 482 pages
File Size : 47,98 MB
Release : 2013-06-29
Category : Science
ISBN : 1475737831

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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.

Author : Marina Axelson-Fisk
Publisher : Springer Science & Business Media
Page : 317 pages
File Size : 37,48 MB
Release : 2010-01-30
Category : Science
ISBN : 1849961042

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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.

Author : Jens Lagergren
Publisher : Springer Science & Business Media
Page : 139 pages
File Size : 15,56 MB
Release : 2005-03-01
Category : Science
ISBN : 3540244557

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This book constitutes the thoroughly refereed post-proceedings of the RECOMB 2004 Satellite Workshop on Comparative Genomics, RCG 2004, held in Bertinoro, Italy in October 2004. The 10 revised full papers presented were carefully reviewed and improved for inclusion in the book. The papers address a broad variety of aspects of comparative genomics ranging from new quantitative discoveries about genome structures and processes to theorems on the complexity of computational problems inspired by genome comparison.

Author : Altuna Akalin
Publisher : CRC Press
Page : 462 pages
File Size : 28,1 MB
Release : 2020-12-16
Category : Mathematics
ISBN : 1498781861

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Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.

Author : Glenn Tesler
Publisher : Springer
Page : 203 pages
File Size : 44,13 MB
Release : 2007-08-30
Category : Science
ISBN : 3540749608

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This book constitutes the refereed proceedings of the 5th RECOMB Comparative Genomics Satellite Workshop, RECOMB-CG 2007, held in San Diego, CA, USA, in September 2007. The 14 revised full papers presented address a broad variety of aspects and components of the field of comparative genomics, ranging from quantitative discoveries about genome structure to algorithms for comparative inference to theorems on the complexity of computational problems required for genome comparison.

Author : Ying Xu
Publisher : World Scientific
Page : 494 pages
File Size : 20,99 MB
Release : 2008
Category : Medical
ISBN : 1860949827

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Over 500 prokaryotic genomes have been sequenced to date, and thousands more have been planned for the next few years. While these genomic sequence data provide unprecedented opportunities for biologists to study the world of prokaryotes, they also raise extremely challenging issues such as how to decode the rich information encoded in these genomes. This comprehensive volume includes a collection of cohesively written chapters on prokaryotic genomes, their organization and evolution, the information they encode, and the computational approaches needed to derive such information. A comparative view of bacterial and archaeal genomes, and how information is encoded differently in them, is also presented. Combining theoretical discussions and computational techniques, the book serves as a valuable introductory textbook for graduate-level microbial genomics and informatics courses.