Bioinformatics in Personalized Medicine

Name: Bioinformatics in Personalized Medicine | 10th Spanish Symposium, JBI 2010, Torremolinos, Spain, October 27-29, 2010. Revised Selected Papers
Brand: Springer
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10th Spanish Symposium, JBI 2010, Torremolinos, Spain, October 27-29, 2010. Revised Selected Papers

Ana Teresa Freitas Arcadi Navarro(Herausgeber*in)

Springer (Verlag)

Erschienen am 28. März 2012

XII, 121 Seiten

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Inhalt

Title page
Preface
Conference Organization
Table of Contents
Statistical Significance for NGS Reads Similarities
Introduction
System and Methods
Results
Discussion
References
Application of Array-Oriented Scientific Data Formats (NetCDF) to Genotype Data, GWASpi as an Example
Introduction
Features
Basic Analysis Features and Procedures
Currently Admitted Formats
Performance
RAM Allocation
Disk Usage
Speed
Implementation
Genotype Data Characteristics
Storage Format Specifications
Array-Oriented Scientific Data Formats
GWASpi's NetCDF-3 Database
Writing Data to a Matrix
Retrieving Data from a Matrix
Other NetCDF-3 Databases Used in GWASpi
Applications, Use Cases and Comparison
Conclusions
References
An Ontology and a REST API for Sequence Based Microbial Typing Data
Introduction
TypOn - Typing Ontology
RESTful Web services
Implementation
Final Remarks
References
Multivariate Methods for the Integration and Visualization of Omics Data
Introduction
Data and Technologies in Modern Molecular Biology
Data Integration: Its Meanings, Goals and Methods
Integration Methodologies
Multiple Factor Analysis
The Problem for the Analysis
Results
Discussion and Conclusions
References
A Holistic Approach for Integrating Genomic Variation Information
Introduction
Locus-Specific Databases
An LSDB Aggregation Web System
Requirements
Architecture
Result
Conclusion
References
SB-KOM: Integration of Pathway Information with BioPax
Introduction
Previous Work
SB-KOM Configuration
Use Cases
Discussion and Conclusions
References
GENote v.ß: AWeb Tool Prototype for Annotation of Unfinished Sequences in Non-model Eukaryotes
Introduction
Implementation
Results and Discussion
Conclusion
References
Interface Similarity Improves Comparison of DNA-Binding Proteins: The Homeobox Example
Introduction
Material and Methods
Homeobox Protein Sequences and DNA Motifs
Structural Alignment of Homeodomains and Identification of Interface Residues
Annotation of Interface Residues in Homeobox Proteins
DNA Motif Alignment and Similarity Scoring
Cross-Validation Parameters
Generating Interface Substitution Matrices (ISUMs)
Pairwise Alignments of Homeobox Domains
Validation of the Calculated ISUMs
Results
Comparison and Clustering of Homeobox Interface Architectures
Defining a Consensus Homeobox Protein-DNA Interface
Derivation of Interface Substitution Matrices (ISUMs)
Evaluation of ISUMs
Limitations of BLASTP Alignments When Predicting Homeobox DNA Motifs
Limitations of Sequence-Based DNA Motif Alignments
Discussion and Conclusions
References
Pyicos: A Flexible Tool Library for Analyzing Protein-Nucleotide Interactions with Mapped Reads from Deep Sequencing
Introduction
Motivation
Results
General Features
Operations
Discussion
References
Novel Angiogenic Functional Targets Predicted through "Dark Matter" Assessment in Protein Networks
Introduction
Results, Conclusions and Methods
Results
Conclusions
Methods
References
jORCA and Magallanes Sailing Together towards Integration of Web Services
Introduction
Service Composition Using jORCA
Discussion
Integration of Magallanes in jORCA
Conclusions
References
iHOP Web Services Family
Introduction
Materials and Methods: iHOP Web Services Evolution
Use Cases
Angiogenic Protein Sub-network
Late Anaphase Chromatin Condensation
References
Bioinformatic Software Developments in Spain
Introduction
INB Bioinformatic Tools and Systems
Web Services
INB Web Services
INB Systems for Working with Web Services
Clinical Data Management
Assessment of Bioinformatic Methods
Software Licensing Issues in Life Sciences
Discussion and Conclusions
References
Author Index

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