Graph algorithms is a well-established subject in mathematics and computer science. Beyond classical application fields, like approximation, combinatorial optimization, graphics, and operations research, graph algorithms have recently attracted increased attention from computational molecular biology and computational chemistry. Centered around the fundamental issue of graph isomorphism, this text goes beyond classical graph problems of shortest paths, spanning trees, flows in networks, and matchings in bipartite graphs. Advanced algorithmic results and techniques of practical relevance...

This book constitutes the refereed proceedings of the 17th Annual Symposium on Combinatorial Pattern Matching, CPM 2006, held in Barcelona, Spain, July 2006. The book presents 33 revised full papers together with 3 invited talks, organized in topical sections on data structures, indexing data structures, probabilistic and algebraic techniques, applications in molecular biology, string matching, data compression, and dynamic programming.

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...