Valiente Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R

Erscheinungsjahr 2010
ISBN: 978-1-4200-6974-7
Verlag: Taylor & Francis
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 368 Seiten

Reihe: Chapman & Hall/CRC Mathematical & Computational Biology

Emphasizing the search for patterns within and between biological sequences, trees, and graphs, Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R shows how combinatorial pattern matching algorithms can solve computational biology problems that arise in the analysis of genomic, transcriptomic, proteomic, metabolomic, and interactomic data. It implements the algorithms in Perl and R, two widely used scripting languages in computational biology.

The book provides a well-rounded explanation of traditional issues as well as an up-to-date account of more recent developments, such as graph similarity and search. It is organized around the specific algorithmic problems that arise when dealing with structures that are commonly found in computational biology, including biological sequences, trees, and graphs. For each of these structures, the author makes a clear distinction between problems that arise in the analysis of one structure and in the comparative analysis of two or more structures. He also presents phylogenetic trees and networks as examples of trees and graphs in computational biology.

This book supplies a comprehensive view of the whole field of combinatorial pattern matching from a computational biology perspective. Along with thorough discussions of each biological problem, it includes detailed algorithmic solutions in pseudo-code, full Perl and R implementation, and pointers to other software, such as those on CPAN and CRAN.

Zielgruppe

Computer scientists, mathematicians, statisticians, and biologists; advanced undergraduate and graduate students in computational biology.

Autoren/Hrsg.

Valiente, Gabriel

Fachgebiete

• Naturwissenschaften Biowissenschaften Biowissenschaften DNA und Transgene Organismen

Inhaltsverzeichnis

Introduction

Combinatorial Pattern Matching

Computational Biology

A Motivating Example: Gene Prediction
SEQUENCE PATTERN MATCHING

Sequences

Sequences in Mathematics
Sequences in Computer Science
Sequences in Computational Biology
Simple Pattern Matching in Sequences

Finding Words in Sequences
General Pattern Matching in Sequences

Finding Subsequences

Finding Common Subsequences

Comparing Sequences
TREE PATTERN MATCHING

Trees

Trees in Mathematics

Trees in Computer Science

Trees in Computational Biology
Simple Pattern Matching in Trees

Finding Paths in Unrooted Trees
Finding Paths in Rooted Trees
General Pattern Matching in Trees

Finding Subtrees

Finding Common Subtrees

Comparing Trees
GRAPH PATTERN MATCHING
Graphs

Graphs in Mathematics

Graphs in Computer Science

Graphs in Computational Biology
Simple Pattern Matching in Graphs

Finding Paths in Graphs

Finding Trees in Graphs
General Pattern Matching in Graphs

Finding Subgraphs

Finding Common Subgraphs

Comparing Graphs
Appendix A: Elements of Perl
Perl Scripts

Overview of Perl

Perl Quick Reference Card
Appendix B: Elements of R
R Scripts

Overview of R

R Quick Reference Card
References
Index
Bibliographic Notes appear at the end of each chapter.

Über Autor(innen)

Gabriel Valiente is Associate Professor in the Department of Software at the Technical University of Catalonia. His research interests include computational biology, bioinformatics, exact and approximate matching in graphs and patterns, and graph transformation.