Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R (Hardcover)

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.

強調在生物序列、樹狀結構和圖形之間尋找模式的《使用Perl和R進行計算生物學的組合模式匹配算法》展示了組合模式匹配算法如何解決在基因組、轉錄組、蛋白質組、代謝組和互作組等數據分析中出現的計算生物學問題。該書使用Perl和R兩種廣泛應用於計算生物學的腳本語言來實現這些算法。

該書全面解釋了傳統問題以及最新發展，如圖形相似性和搜索。它圍繞在計算生物學中常見的結構（包括生物序列、樹狀結構和圖形）處理時出現的特定算法問題組織。對於每個結構，作者清楚區分了在分析單一結構和比較分析兩個或多個結構時出現的問題。他還以系統發生樹和網絡作為計算生物學中樹狀結構和圖形的示例。

該書從計算生物學的角度提供了對組合模式匹配整個領域的全面觀點。除了對每個生物問題進行詳細討論外，它還包括偽代碼的詳細算法解決方案、完整的Perl和R實現，以及指向其他軟件（如CPAN和CRAN上的軟件）的指針。