Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R

Abstract

Emphasizing the search for patterns within and between biological sequences, trees, and graphs, this book 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 provides an intuitive presentation of the algorithms, followed by a detailed exposition in pseudo-code. The author offers alternative implementations of the algorithms in Perl and R to enable the testing of algorithms and the building of projects based on the code. He also includes the Perl and R source code for all the algorithms on his website.