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Algorithms in bioinformatics : 7th international workshop, WABI 2007, Philadelphia, PA, USA, September 8-9, 2007 : proceedings / Raffaele Giancarlo, Sridhar Hannenhalli (eds.).

By: Contributor(s): Material type: TextTextSeries: LNCS sublibrary. SL 8, Bioinformatics. | Lecture notes in computer science ; 4645. | Lecture notes in computer science. Lecture notes in bioinformatics.Publication details: Berlin ; New York : Springer, ©2007.Description: 1 online resource (xiii, 432 pages) : illustrationsContent type:
  • text
Media type:
  • computer
Carrier type:
  • online resource
ISBN:
  • 9783540741268
  • 3540741267
  • 9783540741251
  • 3540741259
Subject(s): Genre/Form: Additional physical formats: Print version:: Algorithms in bioinformatics.DDC classification:
  • 572.80285 22
LOC classification:
  • QH324.2 .W32 2007eb
NLM classification:
  • 2007 J-900
  • QU 26.5
Other classification:
  • Q811. 4-532
Online resources:
Contents:
Intro -- Title Page -- Preface -- Organization -- Table of Contents -- Shotgun Protein Sequencing -- Locality Kernels for Protein Classification -- Introduction -- Regularized Least-Squares Algorithm -- Locality Kernels -- Spectrum and Mismatch Kernels -- Experiments -- Conclusions -- References -- When Less Is More: Improving Classification of Protein Families with a Minimal Set of Global Features -- Introduction -- DataandMethods -- Data -- Preprocessing -- Classification -- Feature Selection -- Evaluation -- Results -- Olfactory Receptor Activity Proteins -- Porin Proteins
Group Size, Selection Method and Success -- Global vs. Local Features -- Combining Local with Global Features -- Discussion -- References -- Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps -- Introduction -- Protein Structure Reconstruction from Contact Maps -- Description of COMAR and FT-COMAR -- Experimental Results -- Conclusions and Perspectives -- References -- Bringing Folding Pathways into Strand Pairing Prediction -- Introduction -- Methods -- ILP Formulation -- Greedy Algorithm with Pathway-Based Promotion -- Results -- Discussion and Conclusions -- References
A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage -- Introduction -- State of the Art -- Our Heuristic -- Experiments -- References -- Two Birds, One Stone: Selecting Functionally Informative Tag SNPs for Disease Association Studies -- Introduction -- Functionally Informative Tag SNP Selection -- Models and Algorithms -- Assessing the Functional Significance of SNPs -- Selecting Functionally Informative Tag SNPs -- Experiments and Results -- Experimental Setting -- Results -- Conclusions -- References
Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity -- Introduction -- Preliminaries -- Hidden Markov Model -- Likelihood Ratio Approach to Error Detection -- Efficiently Computable Likelihood Functions -- Viterbi Probability -- Probability of Viterbi Haplotypes -- Total Trio Genotype Probability -- Experimental Results -- Experimental Setup -- Results on Synthetic Datasets -- Results on Real Data from [13] -- Conclusions -- References -- Haplotype Inference Via Hierarchical Genotype Parsing -- Introduction -- Genotypes, Haplotypes, and Recombination
Combinatorial Mosaic Model -- Hardness of Finding Founders -- Heuristic Algorithm for Founder Construction -- Hierarchical Parsing -- Experimental Results -- References -- Seeded Tree Alignment and Planar Tanglegram Layout -- Introduction -- Tree Alignment Based on Seeded Nodes -- Planar Tanglegram Layout -- References -- Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion -- Introduction -- Definitions -- Hardness Issues -- Algorithms and Parameters -- Experimental Results -- Biological Inputs: Proteins and Genes
Summary: This book constitutes the refereed proceedings of the 7th International Workshop on Algorithms in Bioinformatics, WABI 2007, held in Philadelphia, PA, USA in September 2007. The 38 revised full papers presented together with the abstract of a keynote talk were carefully reviewed and selected from 133 submissions. All current issues of algorithms in bioinformatics are addressed, ranging from mathematical tools to experimental studies of approximation algorithms and reports on significant computational analyses. Numerous biological problems are dealt with, including genetic mapping, sequence alignment and sequence analysis, phylogeny, comparative genomics, and protein structure. Furthermore the papers feature high-performance computing approaches to computationally hard learning and optimization problems in bioinformatics and cover methods, software and dataset repositories for development and testing of such algorithms and their underlying models.
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eBook eBook e-Library eBook LNCS Available
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Includes bibliographical references.

Print version record.

This book constitutes the refereed proceedings of the 7th International Workshop on Algorithms in Bioinformatics, WABI 2007, held in Philadelphia, PA, USA in September 2007. The 38 revised full papers presented together with the abstract of a keynote talk were carefully reviewed and selected from 133 submissions. All current issues of algorithms in bioinformatics are addressed, ranging from mathematical tools to experimental studies of approximation algorithms and reports on significant computational analyses. Numerous biological problems are dealt with, including genetic mapping, sequence alignment and sequence analysis, phylogeny, comparative genomics, and protein structure. Furthermore the papers feature high-performance computing approaches to computationally hard learning and optimization problems in bioinformatics and cover methods, software and dataset repositories for development and testing of such algorithms and their underlying models.

Intro -- Title Page -- Preface -- Organization -- Table of Contents -- Shotgun Protein Sequencing -- Locality Kernels for Protein Classification -- Introduction -- Regularized Least-Squares Algorithm -- Locality Kernels -- Spectrum and Mismatch Kernels -- Experiments -- Conclusions -- References -- When Less Is More: Improving Classification of Protein Families with a Minimal Set of Global Features -- Introduction -- DataandMethods -- Data -- Preprocessing -- Classification -- Feature Selection -- Evaluation -- Results -- Olfactory Receptor Activity Proteins -- Porin Proteins

Group Size, Selection Method and Success -- Global vs. Local Features -- Combining Local with Global Features -- Discussion -- References -- Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps -- Introduction -- Protein Structure Reconstruction from Contact Maps -- Description of COMAR and FT-COMAR -- Experimental Results -- Conclusions and Perspectives -- References -- Bringing Folding Pathways into Strand Pairing Prediction -- Introduction -- Methods -- ILP Formulation -- Greedy Algorithm with Pathway-Based Promotion -- Results -- Discussion and Conclusions -- References

A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage -- Introduction -- State of the Art -- Our Heuristic -- Experiments -- References -- Two Birds, One Stone: Selecting Functionally Informative Tag SNPs for Disease Association Studies -- Introduction -- Functionally Informative Tag SNP Selection -- Models and Algorithms -- Assessing the Functional Significance of SNPs -- Selecting Functionally Informative Tag SNPs -- Experiments and Results -- Experimental Setting -- Results -- Conclusions -- References

Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity -- Introduction -- Preliminaries -- Hidden Markov Model -- Likelihood Ratio Approach to Error Detection -- Efficiently Computable Likelihood Functions -- Viterbi Probability -- Probability of Viterbi Haplotypes -- Total Trio Genotype Probability -- Experimental Results -- Experimental Setup -- Results on Synthetic Datasets -- Results on Real Data from [13] -- Conclusions -- References -- Haplotype Inference Via Hierarchical Genotype Parsing -- Introduction -- Genotypes, Haplotypes, and Recombination

Combinatorial Mosaic Model -- Hardness of Finding Founders -- Heuristic Algorithm for Founder Construction -- Hierarchical Parsing -- Experimental Results -- References -- Seeded Tree Alignment and Planar Tanglegram Layout -- Introduction -- Tree Alignment Based on Seeded Nodes -- Planar Tanglegram Layout -- References -- Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion -- Introduction -- Definitions -- Hardness Issues -- Algorithms and Parameters -- Experimental Results -- Biological Inputs: Proteins and Genes

English.

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