Combinatorial pattern matching algorithms in computational biology using Perl and R / Gabriel Valiente. — Boca Raton : CRC Press, c2009. – (58.1057/V172)

Contents

    Contents
    
    Foreword
    Preface
    1 Introduction
    1.1 Combinatorial Pattern Matching
    1.2 Computational Biology
    1.3 A Motivating Example: Gene Prediction
    Bibliographic Notes
    I Sequence Pattern Matching
    2 Sequences
    2.1 Sequences in Mathematics
    2.2 Sequences in Computer Science
    2.3 Sequences in Computational Biology
    Bibliographic Notes
    3 Simple Pattern Matching in Sequences
    3.1 Finding Words in Sequences
    Bibliographic Notes
    4 General Pattern Matching in Sequences
    4.1 Finding Subsequences
    4.2 Finding Common Subsequences
    4.3 Comparing Sequences
    Bibliographic Notes
    II Tree Pattern Matching
    5 Trees
    5.1 Trees in Mathematics
    5.2 Trees in Computer Science
    5.3 Trees in Computational Biology
    Bibliographic Notes
    6 Simple Pattern Matching in Trees
    6.1 Finding Paths in Unrooted Trees
    6.2 Finding Paths in Rooted Trees
    Bibliographic Notes
    7 General Pattern Matching in Trees
    7.1 Finding Subtrees
    7.2 Finding Common Subtrees
    7.3 Comparing Trees
    Bibliographic Notes
    III Graph Pattern Matching
    8 Graphs
    8.1 Graphs in Mathematics
    8.2 Graphs in Computer Science
    8.3 Graphs in Computational Biology
    Bibliographic Notes
    9 Simple Pattern Matching in Graphs
    9.1 Finding Paths in Graphs
    9.2 Finding Trees in Graphs
    Bibliographic Notes
    10 General Pattern Matching in Graphs
    10.1 Finding Subgraphs
    10.2 Finding Common Subgraphs
    10.3 Comparing Graphs
    Bibliographic Notes
    A Elements of Perl
    A.1 Perl Scripts
    A.2 Overview of Perl
    A.3 Perl Quick Reference Card
    Bibliographic Notes
    B Elements of R
    B.1 R Scripts
    B.2 Overview of R
    B.3 R Quick Reference Card
    Bibliographic Notes
    References
    Index