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检索条件"任意字段=16th International Conference on DNA Computing and Molecular Programming"

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Separating repeats in dna sequence assembly 01

Separating repeats in DNA sequence assembly

引用

5th Annual Internatinal conference on Computational Biology

作者： Kececioglu, J. Yu, J. Department of Computer Science University of Arizona Tucson AZ 85721-0077 United States

ISBN: (纸本)9781581133530

One of the key open problems in large-scale dna sequence assembly is the correct reconstruction of sequences that contain repeats. A long repeat can confound a sequence assembler into falsely overlaying fragments that sample its copies, effectively compressing out the repeat in the reconstructed sequence. We call the task of correcting this compression by separating the overlaid fragments into the distinct copies they sample, the repeat separation problem. We present a rigorous formulation of repeat separation in the general setting without prior knowledge of consensus sequences of repeats or their number of copies. Our formulation decomposes the task into a series of four subproblems, and we design probabilistic tests or combinatorial algorithms that solve each subproblem. the core subproblem separates repeats using the so-called k-median problem in combinatorial optimization, which we solve using integer linear-programming. Experiments with an implementation show we can separate fragments that are over laid at 10 times the coverage with very few mistakes in a few seconds of computation, even when the sequencing error rate and the error rate between copies are identical. To our knowledge this is the first rigorous and fully general approach to separating repeats that directly addresses the problem.

关键词： dna sequences

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Sequence Assembly Validation by Multiple Restriction Digest Fragment Coverage Analysis

Sequence Assembly Validation by Multiple Restriction Digest ...

引用

6th international conference on Intelligent Systems for molecular Biology, ISMB 1998

作者： Rouchka, Eric C. States, David J. Institute for Biomedical Computing Washington University 700 South Euclid Avenue St. LouisMO63110-1012 United States

ISBN: (纸本)1577350537

dna sequence analysis depends on the accurate assembly of fragment reads for the determination of a consensus sequence. this report examines the possibility of analyzing multiple, independent restriction digests as a method for testing the fidelity of sequence assembly. A dynamic programming algorithm to determine the maximum likelihood alignment of error prone electrophoretic mobility data to the expected fragment mobilities given the consensus sequence and restriction enzymes is derived and used to assess the likelihood of detecting rearrangements in genonúc sequencing projects. the method is shown to reliably detect errors in sequence fragment assembly without the necessity of making reference to an overlying physical map. An html form-based interface is available at http://***/services/***. © 1998, AAAI (***). All rights reserved.

关键词： Dynamic programming

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Proceedings of the 27th Hawaii international conference on System Sciences (HICSS-27). Part 5 (of 5)

Proceedings of the 27th Hawaii International Conference on S...

引用

the 27th Hawaii international conference on System Sciences, HICSS-27

ISBN: (纸本)0818650907

the proceedings contains 47 papers on the applications of computing to natural sciences. Topics discussed include dna sequences, proteins, biology, data structures, databases, computer systems, algorithms, molecular structures, genomes, data reduction, drugs, computer programming, computer programming languages, user interfaces, computer graphics and systems analysis.

关键词： Natural sciences computing

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the role of high performance parallel computing in biological research [molecular structure application]

The role of high performance parallel computing in biologica...

引用

Annual international conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： R.L. Martino C.A. Johnson E.B. Suh B.L. Trus T.K. Yap Computational Bioscience and Engineering Laboratory Computer Research and Technology National Institutes of Health DHHS Bethesda MD USA

Scalable parallel computer architectures provide the computational performance demanded by advanced biological computing problems. NIH has developed a number of parallel algorithms and techniques useful in determining biological structure and function. these applications include processing electron micrographs to determine the three-dimensional structure of viruses, calculating the solvent accessible surface area of proteins to predict the three-dimensional conformation of these molecules from their primary structure, and searching for homologous dna sequences in large genetic databases. Timing results demonstrate substantial performance improvements with parallel implementations compared with conventional sequential systems.

关键词： Parallel processing Biology computing Concurrent computing Computer architecture Parallel algorithms Application software Electrons Viruses (medical) Solvents Proteins

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dna computing and molecular programming 1

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丛书名： Lecture Notes in Computer Science

1000年

作者： David Soloveichik Bernard Yurke

ISBN: (数字)9783319019284

ISBN: (纸本)9783319019277

this book constitutes the refereed proceedings of the 19th international conference on dna computing and molecular programming, dna 19, held in Tempe, AZ, USA, in September 2013. the 14 full papers presented were carefully selected from 29 submissions. the papers are organized in many disciplines (including mathematics, computer science, physics, chemistry, material science and biology) to address the analysis, design, and synthesis of information-based molecular systems.

关键词： Computation by Abstract Devices Algorithm Analysis and Problem Complexity Computational Biology/Bioinformatics Artificial Intelligence Data Structures Discrete Mathematics in Computer Science

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dna computing and molecular programming 1

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丛书名： Lecture Notes in Computer Science

1000年

作者： Robert Brijder Lulu Qian

ISBN: (数字)9783319667997

ISBN: (纸本)9783319667980

this book constitutes the refereed proceedings of the 23th international conference on dna computing and molecular programming, dna 23, held Austin, TX, USA, in September 2017. the 16 full papers presented were carefully selected from 23 submissions. Research in dna computing aims to draw together mathematics, computerscience, physics, chemistry, biology, and nanotechnology to address the analysis, design, and synthesis of information-based molecular systems. the papers address all areas related to biomolecular computing such as: algorithms and models for computation with biomolecular systems; computational processes in vitro and in vivo; molecular motors and molecular robotics; studies of fault-tolerance and error correction; software tools for analysis, simulation, and design; synthetic biology and in vitro evolution; applications in engineering, physics, chemistry, biology, and medicine.

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Bio-Inspired computing: theories and Applications 1

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丛书名： Communications in Computer and Information Science

1000年

作者： Linqiang Pan Lianghao Li Zhihua Cui Jianghui Cai

ISBN: (数字)9789811912535

ISBN: (纸本)9789811912528

this two-volume set (CCIS 1565 and CCIS 1566) constitutes selected and revised papers from the 16th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2021, held in Taiyuan, China, in December 2021.;the 67 papers presented were thoroughly reviewed and selected from 211 submissions. the papers are organized in the following topical sections: evolutionary computation and swarm intelligence; dna and molecular computing; machine learning and computer vision.

关键词： Image Processing and Computer Vision Artificial Intelligence Computer System Implementation Computer Communication Networks Information Systems and Communication Service Computer Appl. in Social and Behavioral Sciences

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dna computing and molecular programming 1

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丛书名： Lecture Notes in Computer Science

1000年

作者： Satoshi Murata Satoshi Kobayashi

ISBN: (数字)9783319112954

ISBN: (纸本)9783319112947

this book constitutes the refereed proceedings of the 20th international conference on dna computing and molecular programming, dna 20, held in Kyoto, Japan, in September 2014. the 10 full papers presented were carefully selected from 55 submissions. the papers are organized in many disciplines (including mathematics, computer science, physics, chemistry, material science and biology) to address the analysis, design, and synthesis of information-based molecular systems.

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dna computing and molecular programming 1

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丛书名： Lecture Notes in Computer Science

1000年

作者： Russell Deaton Akira Suyama

ISBN: (数字)9783642106040

ISBN: (纸本)9783642106033

this book constitutes the thoroughly refereed post-conference proceedings of the 15th international Meeting on dna computing, dna15, held in Fayetteville, AR, USA, in June 2009. the 16 revised full papers presented were carefully selected during two rounds of reviewing and improvement from 38 submissions. the papers feature current interdisciplinary research in molecular-scale manipulation of matter - in particular, implementation of nanoscale computation and programmed assembly of materials are of interest, thus reflecting a broader scope beyond dna-based nanotechnology and computation.

关键词： theory of Computation Biochemistry, general Nanotechnology and Microengineering Computation by Abstract Devices Algorithm Analysis and Problem Complexity Computational Biology/Bioinformatics

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dna computing and molecular programming 1

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丛书名： Lecture Notes in Computer Science

1000年

作者： Luca Cardelli William Shih

ISBN: (数字)9783642236389

ISBN: (纸本)9783642236372

this book constitutes the refereed proceedings of the 17th international conference on dna computing and molecular programming, dna17, held in Pasadena, CA, USA, in September 2011.;the 12 revised full papers presented together with 5 invited talks were carefully selected from numerous submissions. Research in dna computing and molecular programming draws together mathematics, computer science, physics, chemistry, biology, and nanotechnology to address the analysis, design, and synthesis of information-based molecular systems. this annual meeting is the premier forum where scientists with diverse backgrounds come together with the common purpose of advancing the engineering and science of biology and chemistry from the point of view of computer science, physics, and mathematics.

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