Beginning Perl For Bioinformatics

Discusses the ties between biology and computer science, how to program, basic PERL programming concepts, and how to use PERL to perform tasks including analyzing genetic codes.

With its highly developed capacity to detect patterns in data, Perl has become one of the most popular languages for biological data analysis. But if you're a biologist with little or no programming experience, starting out in Perl can be a challenge. Many biologists have a difficult time learning how to apply the language to bioinformatics. The most popular Perl programming books are often too theoretical and too focused on computer science for a non-programming biologist who needs to solve very specific problems.Beginning Perl for Bioinformatics is designed to get you quickly over the Perl language barrier by approaching programming as an important new laboratory skill, revealing Perl programs and techniques that are immediately useful in the lab. Each chapter focuses on solving a particular bioinformatics problem or class of problems, starting with the simplest and increasing in complexity as the book progresses. Each chapter includes programming exercises and teaches bioinformatics by showing and modifying programs that deal with various kinds of practical biological problems. By the end of the book you'll have a solid understanding of Perl basics, a collection of programs for such tasks as parsing BLAST and GenBank, and the skills to take on more advanced bioinformatics programming. Some of the later chapters focus in greater detail on specific bioinformatics topics. This book is suitable for use as a classroom textbook, for self-study, and as a reference.The book covers: Programming basics and working with DNA sequences and strings Debugging your code Simulating gene mutations using random number generators Regular expressions and finding motifs in data Arrays, hashes, and relational databases Regular expressions and restriction maps Using Perl to parse PDB records, annotations in GenBank, and BLAST output

Historically, programming hasn't been considered a critical skill for biologists. But now, with access to vast amounts of biological data contained in public databases, programming skills are increasingly in strong demand in biology research and development. Perl, with its highly developed capacities in string handling, text processing, networking, and rapid prototyping, has emerged as the programming language of choice for biological data analysis.Mastering Perl for Bioinformatics covers the core Perl language and many of its module extensions, presenting them in the context of biological data and problems of pressing interest to the biological community. This book, along with Beginning Perl for Bioinformatics, forms a basic course in Perl programming. This second volume finishes the basic Perl tutorial material (references, complex data structures, object-oriented programming, use of modules--all presented in a biological context) and presents some advanced topics of considerable interest in bioinformatics.The range of topics covered in Mastering Perl for Bioinformatics prepares the reader for enduring and emerging developments in critical areas of bioinformatics programming such as: Gene finding String alignment Methods of data storage and retrieval (SML and databases) Modeling of networks (graphs and Petri nets) Graphics (Tk) Parallelization Interfacing with other programming languages Statistics (PDL) Protein structure determination Biological models of computation (DNA Computers) Biologists and computer scientists who have conquered the basics of Perl and are ready to move even further in their mastery of this versatile language will appreciate the author's well-balanced approach to applying Perl's analytical abilities to the field of bioinformatics. Full of practical examples and real-world biological problem solving, this book is a must for any reader wanting to move beyond beginner level Perl in bioinformatics.

Working on the assumption that the reader has no formal training in programming, Perl Programming for Biologists demonstrates how Perl is used to solve biological problems. Each chapter opens with a set of learning objectives, provides numerous review questions and self-study exercises, and concludes with a bulleted summary of key points. The author incorporates numerous real-life examples throughout the text. Upon completing the book, readers are able to quickly perform such tasks as correcting recurring errors in spreadsheets, scanning a Fasta sequence for every occurrence of an EcoRI site, adapting other writers' scripts to one's own purposes, and most important, writing reusable and maintainable scripts that spare the rote repetition of code.

This is a book for those of us who believed that we didn’t need to learn Perl, and now we know it is more ubiquitous than ever. Perl is extremely flexible and powerful, and it isn’t afraid of Web 2.0 or the cloud. Originally touted as the duct tape of the Internet, Perl has since evolved into a multipurpose, multiplatform language present absolutely everywhere: heavy-duty web applications, the cloud, systems administration, natural language processing, and financial engineering. Beginning Perl, Third Edition provides valuable insight into Perl’s role regarding all of these tasks and more. Commencing with a comprehensive overview of language basics, you’ll learn all about important concepts such as Perl’s data types and control flow constructs. This material sets the stage for a discussion of more complex topics, such as writing custom functions, using regular expressions, and file input and output. Next, the book moves on to the advanced topics of object-oriented programming, modules, web programming, and database administration with Perl’s powerful database interface module, DBI. The examples and code provided offer you all of the information you need to start writing your own powerful scripts to solve the problems listed above, and many more. Whether you are a complete novice or an experienced programmer, Beginning Perl, Third Edition offers an ideal guide to learning Perl.

The sixth edition of this bestselling Perl tutorial includes recent changes to the language. Years of classroom testing and experience helped shape the book's pace and scope, and this edition is packed with exercises that let readers practice the concepts while they follow the text.

An accessible guide to learning the key features of Unix and Perl, written with the non-programmer in mind.