Parameter Advising for Multiple Sequence Alignment PDF Download
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Author: Dan DeBlasio
Publisher: Springer
ISBN: 3319649183
Category : Computers
Languages : en
Pages : 152
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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 : 152
Get Book
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: Theodor Sperlea
Publisher: Springer
ISBN: 9783662644720
Category : Science
Languages : en
Pages : 103
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Book Description
This book is a practical guide for biologists who use multiple sequence alignments (MSAs) for their data analysis and are looking for a comprehensive overview of the many different programs. Despite their important role in data analysis, there is uncertainty among researchers about exactly how MSA programs work - not to mention how and why the different analyzes lead to different results. Which program is the right one for evaluating my data and how can I ensure that I have drawn all relevant findings from the alignments? This book offers helpful explanations and background information without requiring extensive bioinformatics knowledge and slowly introduces the reader to the topic.In the first part of the book, the possible fields of application as well as the formats that are usually produced by MSA programs are described in detail. The central algorithms as well as the internal processes of the most common MSA programs of the past and the present are also explained in an uncomplicated manner in greater detail. The second part of the book is a detailed, data-based comparison between MSA programs, which is intended to help you decide which program to use for your next alignment.
Author: David J Russell
Publisher: Humana
ISBN: 9781493960477
Category : Science
Languages : en
Pages : 0
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Book Description
From basic performing of sequence alignment through a proficiency at understanding how most industry-standard alignment algorithms achieve their results, Multiple Sequence Alignment Methods describes numerous algorithms and their nuances in chapters written by the experts who developed these algorithms. The various multiple sequence alignment algorithms presented in this handbook give a flavor of the broad range of choices available for multiple sequence alignment generation, and their diversity is a clear reflection of the complexity of the multiple sequence alignment problem and the amount of information that can be obtained from multiple sequence alignments. Each of these chapters not only describes the algorithm it covers but also presents instructions and tips on using their implementation, as is fitting with its inclusion in the highly successful Methods in Molecular Biology series. Authoritative and practical, Multiple Sequence Alignment Methods provides a readily available resource which will allow practitioners to experiment with different algorithms and find the particular algorithm that is of most use in their application.
Author: Jin Xiong
Publisher: Cambridge University Press
ISBN: 113945062X
Category : Science
Languages : en
Pages : 360
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Book Description
Essential Bioinformatics is a concise yet comprehensive textbook of bioinformatics, which provides a broad introduction to the entire field. Written specifically for a life science audience, the basics of bioinformatics are explained, followed by discussions of the state-of-the-art computational tools available to solve biological research problems. All key areas of bioinformatics are covered including biological databases, sequence alignment, genes and promoter prediction, molecular phylogenetics, structural bioinformatics, genomics and proteomics. The book emphasizes how computational methods work and compares the strengths and weaknesses of different methods. This balanced yet easily accessible text will be invaluable to students who do not have sophisticated computational backgrounds. Technical details of computational algorithms are explained with a minimum use of mathematical formulae; graphical illustrations are used in their place to aid understanding. The effective synthesis of existing literature as well as in-depth and up-to-date coverage of all key topics in bioinformatics make this an ideal textbook for all bioinformatics courses taken by life science students and for researchers wishing to develop their knowledge of bioinformatics to facilitate their own research.
Author: Richard Durbin
Publisher: Cambridge University Press
ISBN: 113945739X
Category : Science
Languages : en
Pages : 372
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Book Description
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.
Author: Theodor Sperlea
Publisher: Springer Nature
ISBN: 3662644738
Category : Science
Languages : en
Pages : 106
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Book Description
This book is a practical guide for biologists who use multiple sequence alignments (MSAs) for their data analysis and are looking for a comprehensive overview of the many different programs. Despite their important role in data analysis, there is uncertainty among researchers about exactly how MSA programs work - not to mention how and why the different analyzes lead to different results. Which program is the right one for evaluating my data and how can I ensure that I have drawn all relevant findings from the alignments? This book offers helpful explanations and background information without requiring extensive bioinformatics knowledge and slowly introduces the reader to the topic.In the first part of the book, the possible fields of application as well as the formats that are usually produced by MSA programs are described in detail. The central algorithms as well as the internal processes of the most common MSA programs of the past and the present are also explained in an uncomplicated manner in greater detail. The second part of the book is a detailed, data-based comparison between MSA programs, which is intended to help you decide which program to use for your next alignment.
Author: Kazutaka Katoh
Publisher: Humana
ISBN: 9781071610350
Category : Science
Languages : en
Pages : 0
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Book Description
Chapter “Alignment of Biological Sequences with Jalview” is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Author: Gautam B. Singh
Publisher: Springer
ISBN: 3319114034
Category : Technology & Engineering
Languages : en
Pages : 345
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Book Description
This book offers comprehensive coverage of all the core topics of bioinformatics, and includes practical examples completed using the MATLAB bioinformatics toolboxTM. It is primarily intended as a textbook for engineering and computer science students attending advanced undergraduate and graduate courses in bioinformatics and computational biology. The book develops bioinformatics concepts from the ground up, starting with an introductory chapter on molecular biology and genetics. This chapter will enable physical science students to fully understand and appreciate the ultimate goals of applying the principles of information technology to challenges in biological data management, sequence analysis, and systems biology. The first part of the book also includes a survey of existing biological databases, tools that have become essential in today’s biotechnology research. The second part of the book covers methodologies for retrieving biological information, including fundamental algorithms for sequence comparison, scoring, and determining evolutionary distance. The main focus of the third part is on modeling biological sequences and patterns as Markov chains. It presents key principles for analyzing and searching for sequences of significant motifs and biomarkers. The last part of the book, dedicated to systems biology, covers phylogenetic analysis and evolutionary tree computations, as well as gene expression analysis with microarrays. In brief, the book offers the ideal hands-on reference guide to the field of bioinformatics and computational biology.
Author:
Publisher:
ISBN:
Category : Amino acid sequence
Languages : en
Pages : 132
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Book Description
Author: Michael S. Rosenberg
Publisher: Univ of California Press
ISBN: 0520256972
Category : Computers
Languages : en
Pages : 357
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Book Description
The sequencing of the human genome involved thousands of scientists but used relatively few tools. Obtaining sequences is simpler, but aligning the sequences remains a complicated but underappreciated aspect of comparative molecular biology. This book discusses the practice of alignment, and the procedures by which alignments are established.
