Combinatorial Pattern Matching Algorithms in Computational Biology using Perl and R

Combinatorial Pattern Matching Algorithms in Computational Biology using Perl and R

by Gabriel Valiente
     
 

ISBN-10: 142006973X

ISBN-13: 9781420069730

Pub. Date: 04/21/2009

Publisher: Taylor & Francis

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

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Overview

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.

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Product Details

ISBN-13:
9781420069730
Publisher:
Taylor & Francis
Publication date:
04/21/2009
Series:
Chapman & Hall/CRC Mathematical and Computational Biology Series
Pages:
368
Product dimensions:
6.20(w) x 9.40(h) x 1.00(d)

Table of Contents

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.

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