An introductory chapter gives background on the biological, mathematical, and computational notions used in the book. Subsequent chapters provide an intuitive presentation of the algorithms, followed by a detailed exposition in pseudo-code.
tacg – a grep for DNA
Material is structured around the specific algorithmic problems when dealing with structures commonly found in computational biology: biological sequences such as DNA, RNA, and protein sequences ; trees such as phylogenetic trees and RNA structures ; and graphs such as phylogenetic networks and signaling pathways. For each of these structures, a clear distinction is made between the problems that arise in the analysis of one structure and the comparative analysis of two or more structures.
Appendices introducing Perl and R are included. Readers are assumed to have some background in mathematics ad computer programming.
Combinatorial pattern matching algorithms in computational biology using Perl and R.
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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.
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