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
ABOUT THE AUTHOR
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| James Tisdall | James Tisdall has worked as a musician, as a programmer and member of technical staff at Bell Labs (where he programmed for speech research and discovered a formal language for musical rhythm), as a programmer and systems manager at the Human Genome Project in the Computational Biology and Informatics Laboratory (where he began using Perl for bioinformatics in 1991 with his program DNA WorkBench), as computational biologist at Mercator Genetics in Menlo Park, California (where his Perl programs helped discover the gene involved in the common hereditary disease hemochromatosis), as manager of Bioinformatics at the Fox Chase Cancer Center in Philadelphia, and most recently as a consultant for Biocomputing Associates of Kimberton, Pennsylvania, and the Burke Research Institute affiliated with Cornell University, working on neurodegenerative diseases such as Alzheimer's and Parkinson's. |
