Format:
Online-Ressource (IX, 627 S.)
,
Ill., graph. Darst.
Edition:
Online-Ausg. 2011 Springer eBook Collection. Mathematics and Statistics Electronic reproduction; Available via World Wide Web
ISBN:
9783642163456
Series Statement:
Springer handbooks of computational statistics
Content:
Numerous fascinating breakthroughs in biotechnology have generated large volumes and diverse types of high throughput data that demand the development of efficient and appropriate tools in computational statistics integrated with biological knowledge and computational algorithms. This volume collects contributed chapters from leading researchers to survey the many active research topics and promote the visibility of this research area. This volume is intended to provide an introductory and reference book for students and researchers who are interested in the recent developments of computational statistics in computational biology.
Note:
Includes bibliographical references
,
Handbook of Statistical Bioinformatics; Foreword; Contents; Part I Sequence Analysis; Chapter 1: Accuracy Assessment of Consensus Sequence from Shotgun Sequencing; 1.1 Introduction; 1.2 Adjustment of Quality Scores from Alignment and Improvement of Sequencing Accuracy; 1.2.1 Sequencing Data; 1.2.2 Setup; 1.2.3 Phred Quality Scores; 1.2.4 Conditional Sequencing Error Model; 1.2.5 Mixture of Logistic Model; 1.2.6 Parameter Estimation and E-M Training Algorithm; 1.2.7 Consensus and Quality Values; 1.2.8 Parsimonious Representation and Model Selection; 1.2.9 Bias of Quality Scores
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1.2.10 Score-Dependent Error Patterns1.2.11 Comparison of Different Methods; 1.3 Reconstruction of Diploid Consensus Sequences and its Accuracy Assessment; 1.3.1 The Probabilistic Model; 1.3.2 A Markov Structure; 1.3.3 Sequencing Error Rates and Quality Scores; 1.3.4 Reconstruction of Diploid Genome; 1.3.5 Mate-Pair Information and Second-Stage Bridging; 1.3.6 Inference of Haplotype Frequency; 1.3.7 An Example; 1.3.8 A Simulation of Human Diploid Genome; 1.3.9 Length of Haplotype Segment and Two-End Sequencing; 1.3.10 Error Patterns; 1.3.11 Confidence Scores for Haplotype Segments
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1.3.12 Gibbs Sampling Algorithm1.3.13 Diploid Genome of Ciona intestinalis and Comparative Genomic Studies; 1.4 Discussion; 1.4.1 Alignment Algorithm; 1.4.2 Computing Complexity; 1.4.3 Repeat Patterns; 1.4.4 Size of Training Data Set; 1.4.5 Next Generation Sequencing; References; Chapter 2: Statistical and Computational Studies on Alternative Splicing; 2.1 Introduction; 2.2 Types of Alternative Splicing; 2.3 Global Identification of Alternative Splicing Events; 2.3.1 Identifying Alternative Splicing by Sequence Alignment
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2.3.2 Identifying Alternative Splicing by Sequence Content and Conservation2.3.3 Identify Alternative Splicing by Microarray; 2.3.3.1 Splicing Index; 2.3.3.2 ANOSVA; 2.3.3.3 FIRMA; 2.3.3.4 DECONV; 2.3.3.5 SPACE; 2.3.3.6 GenASAP; 2.3.4 Identify Alternative Splicing by High Throughput Sequencing; 2.4 Alternative Splicing Regulation in Eukaryotes; 2.5 Alternative Splicing, Genetic Variation, and Disease; 2.6 Online Resources; 2.7 Summary; References; Chapter 3: Statistical Learning and Modeling of TF-DNA Binding; 3.1 Introduction; 3.2 Experimental Methods for Identifying TF-DNA Interactions
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3.3 Generative Models for Discovering TF Binding Motifs3.3.1 Motif Formulations and General Discovery Strategies; 3.3.2 A Block-Motif Model for Finding Motifs in a Set of Sequences; 3.3.3 Comparative Genomic Approach for TF Binding Sites Discovery; 3.3.4 Hidden Markov Models for Cis-regulatory Module Discovery; 3.3.5 Motif Discovery in ChIP-Array Experiments; 3.4 Predictive Models for TF-DNA Interaction; 3.4.1 Joint Analysis of Sequence Motifs and Expression Microarrays; 3.4.2 Modeling TF-DNA Interaction and Genome-wide Occupancy Data
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3.4.3 Selecting Sequence Features to Predict TF-DNA Interactions
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Electronic reproduction; Available via World Wide Web
Additional Edition:
ISBN 9783642163449
Additional Edition:
Druckausg. Handbook of statistical bioinformatics Berlin : Springer, 2011 ISBN 3642163440
Additional Edition:
ISBN 9783642163449
Language:
English
Subjects:
Biology
Keywords:
Bioinformatik
;
Statistik
DOI:
10.1007/978-3-642-16345-6
URL:
Volltext
(lizenzpflichtig)
URL:
Volltext
(lizenzpflichtig)
Author information:
Schölkopf, Bernhard 1968-
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