Perl for Bioinformatics

This short book is aimed at biologists interested in simple programming for their tasks, and for computer scientists interested in learning about biomolecular problems and issues, and seeing tailored programming solutions to them. Part I introduces relevant Perl basics: data types, control structures, input and output, regular expressions, handy functions on strings, and subroutines, all with illustrative examples from bioinformatics. Part II is organized as follows: Chapter 7 presents several Perl scripts for various common bioinformatics tasks. Chapter 8 describes several bioinformatics algorithms used in fragment assembly, heuristic local alignment, automated motif discovery, classification of sequences, optimal sequence-to-sequence alignment, optimal sequence-to-profile alignment, heuristic multiple alignment, profile hidden Markov models, and phylogenetic analysis and presents Perl scripts for them. Chapter 9 covers the BioPerl project. Chapter 10 covers some Perl modules of use in bioinformatics.