Repetitive Structures In Biological Sequences Algorithms And Applications

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Repetitive Structures in Biological Sequences: Algorithms and Applications

Author : Marco Pellegrini
Publisher : Frontiers Media SA
ISBN 13 : 288945018X
Total Pages : 95 pages
Book Rating : 4.8/5 (894 download)

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Book Synopsis Repetitive Structures in Biological Sequences: Algorithms and Applications by : Marco Pellegrini

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.

Repetitive Structures in Biological Sequences and Applications in High Throughput Technologies

Author : Pavlos Antoniou
Publisher :
ISBN 13 :
Total Pages : 400 pages
Book Rating : 4.:/5 (681 download)

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Book Synopsis Repetitive Structures in Biological Sequences and Applications in High Throughput Technologies by : Pavlos Antoniou

Download or read book Repetitive Structures in Biological Sequences and Applications in High Throughput Technologies written by Pavlos Antoniou and published by . This book was released on 2009 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt:

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.

Efficient Algorithms for Identification and Analysis of Repetitive Patterns in Biological Sequences

Author : Jie Zheng
Publisher :
ISBN 13 :
Total Pages : 224 pages
Book Rating : 4.3/5 (121 download)

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Book Synopsis Efficient Algorithms for Identification and Analysis of Repetitive Patterns in Biological Sequences by : Jie Zheng

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:

Genome-Scale Algorithm Design

Author : Veli Mäkinen
Publisher : Cambridge University Press
ISBN 13 : 1316342948
Total Pages : 415 pages
Book Rating : 4.3/5 (163 download)

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Book Synopsis Genome-Scale Algorithm Design by : Veli Mäkinen

Download or read book Genome-Scale Algorithm Design written by Veli Mäkinen and published by Cambridge University Press. This book was released on 2015-05-07 with total page 415 pages. Available in PDF, EPUB and Kindle. Book excerpt: High-throughput sequencing has revolutionised the field of biological sequence analysis. Its application has enabled researchers to address important biological questions, often for the first time. This book provides an integrated presentation of the fundamental algorithms and data structures that power modern sequence analysis workflows. The topics covered range from the foundations of biological sequence analysis (alignments and hidden Markov models), to classical index structures (k-mer indexes, suffix arrays and suffix trees), Burrows–Wheeler indexes, graph algorithms and a number of advanced omics applications. The chapters feature numerous examples, algorithm visualisations, exercises and problems, each chosen to reflect the steps of large-scale sequencing projects, including read alignment, variant calling, haplotyping, fragment assembly, alignment-free genome comparison, transcript prediction and analysis of metagenomic samples. Each biological problem is accompanied by precise formulations, providing graduate students and researchers in bioinformatics and computer science with a powerful toolkit for the emerging applications of high-throughput sequencing.

Identification and Application of Repetitive Biological Sequences

Author : Xuehui Li
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (663 download)

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Book Synopsis Identification and Application of Repetitive Biological Sequences by : Xuehui Li

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.

Pattern Discovery in Biomolecular Data

Author : Jason T. L. Wang
Publisher : Oxford University Press
ISBN 13 : 0190283726
Total Pages : 272 pages
Book Rating : 4.1/5 (92 download)

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Book Synopsis Pattern Discovery in Biomolecular Data by : Jason T. L. Wang

Download or read book Pattern Discovery in Biomolecular Data written by Jason T. L. Wang and published by Oxford University Press. This book was released on 1999-10-28 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: Finding patterns in biomolecular data, particularly in DNA and RNA, is at the center of modern biological research. These data are complex and growing rapidly, so the search for patterns requires increasingly sophisticated computer methods. Pattern Discovery in Biomolecular Data provides a clear, up-to-date summary of the principal techniques. Each chapter is self-contained, and the techniques are drawn from many fields, including graph theory, information theory, statistics, genetic algorithms, computer visualization, and vision. Since pattern searches often benefit from multiple approaches, the book presents methods in their purest form so that readers can best choose the method or combination that fits their needs. The chapters focus on finding patterns in DNA, RNA, and protein sequences, finding patterns in 2D and 3D structures, and choosing system components. This volume will be invaluable for all workers in genomics and genetic analysis, and others whose research requires biocomputing.

Biological Sequence Analysis Using the SeqAn C++ Library

Author : Andreas Gogol-Döring
Publisher : CRC Press
ISBN 13 : 1420076248
Total Pages : 330 pages
Book Rating : 4.4/5 (2 download)

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Book Synopsis Biological Sequence Analysis Using the SeqAn C++ Library by : Andreas Gogol-Döring

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

Field Programmable Logic and Application

Author : Jürgen Becker
Publisher : Springer Science & Business Media
ISBN 13 : 3540229892
Total Pages : 1226 pages
Book Rating : 4.5/5 (42 download)

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Book Synopsis Field Programmable Logic and Application by : Jürgen Becker

Download or read book Field Programmable Logic and Application written by Jürgen Becker and published by Springer Science & Business Media. This book was released on 2004-08-19 with total page 1226 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 14th International Conference on Field-Programmable Logic, FPL 2003, held in Leuven, Belgium in August/September 2004. The 78 revised full papers, 45 revised short papers, and 29 poster abstracts presented together with 3 keynote contributions and 3 tutorial summaries were carefully reviewed and selected from 285 papers submitted. The papers are organized in topical sections on organic and biologic computing, security and cryptography, platform-based design, algorithms and architectures, acceleration application, architecture, physical design, arithmetic, multitasking, circuit technology, network processing, testing, applications, signal processing, computational models and compiler, dynamic reconfiguration, networks and optimisation algorithms, system-on-chip, high-speed design, image processing, network-on-chip, power-aware design, IP-based design, co-processing architectures, system level design, physical interconnect, computational models, cryptography and compression, network applications and architecture, and debugging and test.

Algorithms on Strings, Trees, and Sequences

Author : Dan Gusfield
Publisher : Cambridge University Press
ISBN 13 : 1139811002
Total Pages : 556 pages
Book Rating : 4.1/5 (398 download)

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Book Synopsis Algorithms on Strings, Trees, and Sequences by : Dan Gusfield

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.

Bioinformatics

Author : Andrzej Polanski
Publisher : Springer Science & Business Media
ISBN 13 : 3540241663
Total Pages : 386 pages
Book Rating : 4.5/5 (42 download)

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Book Synopsis Bioinformatics by : Andrzej Polanski

Download or read book Bioinformatics written by Andrzej Polanski and published by Springer Science & Business Media. This book was released on 2007-04-19 with total page 386 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook presents mathematical models in bioinformatics and describes biological problems that inspire the computer science tools used to manage the enormous data sets involved. The first part of the book covers mathematical and computational methods, with practical applications presented in the second part. The mathematical presentation avoids unnecessary formalism, while remaining clear and precise. The book closes with a thorough bibliography, reaching from classic research results to very recent findings. This volume is suited for a senior undergraduate or graduate course on bioinformatics, with a strong focus on mathematical and computer science background.

Algorithms in Computational Molecular Biology

Author : Mourad Elloumi
Publisher : John Wiley & Sons
ISBN 13 : 1118101987
Total Pages : 1027 pages
Book Rating : 4.1/5 (181 download)

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Book Synopsis Algorithms in Computational Molecular Biology by : Mourad Elloumi

Download or read book Algorithms in Computational Molecular Biology written by Mourad Elloumi and published by John Wiley & Sons. This book was released on 2011-04-04 with total page 1027 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book represents the most comprehensive and up-to-date collection of information on the topic of computational molecular biology. Bringing the most recent research into the forefront of discussion, Algorithms in Computational Molecular Biology studies the most important and useful algorithms currently being used in the field, and provides related problems. It also succeeds where other titles have failed, in offering a wide range of information from the introductory fundamentals right up to the latest, most advanced levels of study.

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.

Soft Computing: Theories and Applications

Author : Tarun K. Sharma
Publisher : Springer Nature
ISBN 13 : 9811616965
Total Pages : 572 pages
Book Rating : 4.8/5 (116 download)

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Book Synopsis Soft Computing: Theories and Applications by : Tarun K. Sharma

Download or read book Soft Computing: Theories and Applications written by Tarun K. Sharma and published by Springer Nature. This book was released on 2021-06-26 with total page 572 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on soft computing and how it can be applied to solve real-world problems arising in various domains, ranging from medicine and healthcare, to supply chain management, image processing and cryptanalysis. It gathers high-quality papers presented at the International Conference on Soft Computing: Theories and Applications (SoCTA 2020), organized online. The book is divided into two volumes and offers valuable insights into soft computing for teachers and researchers alike; the book will inspire further research in this dynamic field.

7th International Conference on Practical Applications of Computational Biology & Bioinformatics

Author : Mohd Saberi Mohamad
Publisher : Springer Science & Business Media
ISBN 13 : 3319005782
Total Pages : 160 pages
Book Rating : 4.3/5 (19 download)

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Book Synopsis 7th International Conference on Practical Applications of Computational Biology & Bioinformatics by : Mohd Saberi Mohamad

Download or read book 7th International Conference on Practical Applications of Computational Biology & Bioinformatics written by Mohd Saberi Mohamad and published by Springer Science & Business Media. This book was released on 2013-04-19 with total page 160 pages. Available in PDF, EPUB and Kindle. Book excerpt: The growth in the Bioinformatics and Computational Biology fields over the last few years has been remarkable and the trend is to increase its pace. In fact, the need for computational techniques that can efficiently handle the huge amounts of data produced by the new experimental techniques in Biology is still increasing driven by new advances in Next Generation Sequencing, several types of the so called omics data and image acquisition, just to name a few. The analysis of the datasets that produces and its integration call for new algorithms and approaches from fields such as Databases, Statistics, Data Mining, Machine Learning, Optimization, Computer Science and Artificial Intelligence. Within this scenario of increasing data availability, Systems Biology has also been emerging as an alternative to the reductionist view that dominated biological research in the last decades. Indeed, Biology is more and more a science of information requiring tools from the computational sciences. In the last few years, we have seen the surge of a new generation of interdisciplinary scientists that have a strong background in the biological and computational sciences. In this context, the interaction of researchers from different scientific fields is, more than ever, of foremost importance boosting the research efforts in the field and contributing to the education of a new generation of Bioinformatics scientists. PACBB‘13 hopes to contribute to this effort promoting this fruitful interaction. PACBB'13 technical program included 19 papers from a submission pool of 32 papers spanning many different sub-fields in Bioinformatics and Computational Biology. Therefore, the conference will certainly have promoted the interaction of scientists from diverse research groups and with a distinct background (computer scientists, mathematicians, biologists). The scientific content will certainly be challenging and will promote the improvement of the work that is being developed by each of the participants.

Bioinformatics Research and Applications

Author : Leonidas Bleris
Publisher : Springer
ISBN 13 : 3642301916
Total Pages : 344 pages
Book Rating : 4.6/5 (423 download)

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Book Synopsis Bioinformatics Research and Applications by : Leonidas Bleris

Download or read book Bioinformatics Research and Applications written by Leonidas Bleris and published by Springer. This book was released on 2012-05-10 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the International Symposium on Bioinformatics Research and Applications, ISBRA 2012, held in Dallas, Texas, USA, in May 2012. The 26 revised full papers presented together with five invited talks were carefully reviewed and selected from 66 submissions. The papers address issues on various aspects of bioinformatics and computational biology and their applications.

Distributed Computing -- IWDC 2004

Author : Nabanita Das
Publisher : Springer
ISBN 13 : 354030536X
Total Pages : 564 pages
Book Rating : 4.5/5 (43 download)

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Book Synopsis Distributed Computing -- IWDC 2004 by : Nabanita Das

Download or read book Distributed Computing -- IWDC 2004 written by Nabanita Das and published by Springer. This book was released on 2004-12-07 with total page 564 pages. Available in PDF, EPUB and Kindle. Book excerpt: Last, but not least, thanks to all the participants and authors. We hope that they enjoyed the workshop as much as the wonderful and culturally vibrant city of Kolkata! Bhabani P. Sinha Indian Statistical Institute, Kolkata, India December 2004 Sajal K. Das University of Texas, Arlington, USA December 2004 Program Chairs’ Message On behalf of the Technical Program Committee of the 6th International Wo- shop on Distributed Computing, IWDC 2004, it was our great pleasure to w- come the attendees to Kolkata, India. Over the last few years, IWDC has emerged as an internationally renowned forum for interaction among researchers from academia and industries around the world. A clear indicator of this fact is the large number of high-quality submissions of technical papers received by the workshop this year. The workshop program consisted of 12 technical sessions with 54 contributed papers, two keynote addresses, four tutorials, a panel, a poster session and the Prof.A.K.ChoudhuryMemorialLecture.TheIWDCProgramCommittee,c- prising 38 distinguished members, worked hard to organize the technical p- gram. Following a rigorous review process, out of 157 submissions only 54 - pers were accepted for presentation in the technical sessions; 27 of the accepted papers were classi?ed as regular papers and the remaining 27 as short papers. Another 11 papers were accepted for presentation in the poster session, each with a one-page abstract appearing in the proceedings.