Parameter Advising for Multiple Sequence Alignment PDF Download
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Author: Dan DeBlasio
Publisher: Springer
ISBN: 3319649183
Category : Computers
Languages : en
Pages : 156
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Book Description
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.
Author: Dan DeBlasio
Publisher: Springer
ISBN: 3319649183
Category : Computers
Languages : en
Pages : 156
Get Book Here
Book Description
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.
Author: S. Cenk Sahinalp
Publisher: Springer
ISBN: 3319569708
Category : Computers
Languages : en
Pages : 420
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Book Description
This book constitutes the proceedings of the 21th Annual Conference on Research in Computational Molecular Biology, RECOMB 2017, held in Hong Kong, China, in May 2017. The 22 regular papers presented in this volume were carefully reviewed and selected from 184 submissions. 16 short abstracts are included in the back matter of the volume. They report on original research in all areas of computational molecular biology and bioinformatics
Author: Martin Frith
Publisher: Springer
ISBN: 3319436813
Category : Computers
Languages : en
Pages : 336
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Book Description
This book constitutes the refereed proceedings of the 16th International Workshop on Algorithms in Bioinformatics, WABI 2016, held in Aarhus, Denmark. The 25 full papers together with 2 invited talks presented were carefully reviewed and selected from 54 submissions. The selected papers cover a wide range of topics from networks, tophylogenetic studies, sequence and genome analysis, comparative genomics, and mass spectrometry data analysis.
Author: Benny Chor
Publisher: Springer
ISBN: 3642296270
Category : Computers
Languages : en
Pages : 388
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Book Description
This book constitutes the refereed proceedings of the 16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012, held in Barcelona, Spain, in April 2012. The 31 revised full papers presented together with 5 keynote lectures were carefully reviewed and selected from 200 submissions. The papers feature current research in all areas of computational molecular biology, including: molecular sequence analysis; recognition of genes and regulatory elements; molecular evolution; protein structure; structural genomics; analysis of gene expression; biological networks; sequencing and genotyping technologies; drug design; probabilistic and combinatorial algorithms; systems biology; computational proteomics; structural and functional genomics; information systems for computational biology and imaging.
Author: Jianyong Qiao
Publisher: Springer
ISBN: 9811328293
Category : Computers
Languages : en
Pages : 508
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Book Description
This two-volume set (CCIS 951 and CCIS 952) constitutes the proceedings of the 13th International Conference on Bio-inspired Computing: Theories and Applications, BIC-TA 2018, held in Beijing, China, in November 2018. The 88 full papers presented in both volumes were selected from 206 submissions. The papers deal with studies abstracting computing ideas such as data structures, operations with data, ways to control operations, computing models from living phenomena or biological systems such as evolution, cells, neural networks, immune systems, swarm intelligence.
Author: Basant K. Tiwary
Publisher: Springer Nature
ISBN: 9811642419
Category : Medical
Languages : en
Pages : 239
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Book Description
This textbook introduces fundamental concepts of bioinformatics and computational biology to the students and researchers in biology, medicine, veterinary science, agriculture, and bioengineering . The respective chapters provide detailed information on biological databases, sequence alignment, molecular evolution, next-generation sequencing, systems biology, and statistical computing using R. The book also presents a case-based discussion on clinical, veterinary, agricultural bioinformatics, and computational bioengineering for application-based learning in the respective fields. Further, it offers readers guidance on reconstructing and analysing biological networks and highlights computational methods used in systems medicine and genome-wide association mapping of diseases. Given its scope, this textbook offers an essential introductory book on bioinformatics and computational biology for undergraduate and graduate students in the life sciences, botany, zoology, physiology, biotechnology, bioinformatics, and genomic science as well as systems biology, bioengineering and the agricultural, and veterinary sciences.
Author: Mohammed I. Khalaf
Publisher: Springer Nature
ISBN: 3030387526
Category : Computers
Languages : en
Pages : 525
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Book Description
This book constitutes the refereed proceedings of the First International Conference on Applied Computing to Support Industry: Innovation and Technology, ACRIT 2019, held in Ramadi, Iraq, in September 2019. The 38 revised full papers and 1 short paper were carefully reviewed and selected from 159 submissions. The papers of this volume are organized in topical sections on theory, methods and tools to support computer science; computer security and cryptography; computer network and communication; real world application in information science and technology.
Author: Tandy Warnow
Publisher: Cambridge University Press
ISBN: 1107184711
Category : Computers
Languages : en
Pages : 399
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Book Description
This book presents the foundations of phylogeny estimation and technical material enabling researchers to develop improved computational methods.
Author: Tim Roughgarden
Publisher: Cambridge University Press
ISBN: 1108494315
Category : Computers
Languages : en
Pages : 705
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Book Description
Introduces exciting new methods for assessing algorithms for problems ranging from clustering to linear programming to neural networks.
Author: Johnny Saldana
Publisher: SAGE
ISBN: 1446200124
Category : Reference
Languages : en
Pages : 282
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Book Description
The Coding Manual for Qualitative Researchers is unique in providing, in one volume, an in-depth guide to each of the multiple approaches available for coding qualitative data. In total, 29 different approaches to coding are covered, ranging in complexity from beginner to advanced level and covering the full range of types of qualitative data from interview transcripts to field notes. For each approach profiled, Johnny Saldaña discusses the method’s origins in the professional literature, a description of the method, recommendations for practical applications, and a clearly illustrated example.
