COVID-19 Response at

Read what we're doing...

Beginning Perl for Bioinformatics


Product Description
Product Details

Table of Contents

Preface. 1. Biology and Computer Science The Organization of DNA The Organization of Proteins In Silico Limits to Computation. 2. Getting Started with Perl A Low and Long Learning Curve Perl's Benefits Installing Perl on Your Computer How to Run Perl Programs Text Editors Finding Help. 3. The Art of Programming Individual Approaches to Programming Edit-Run-Revise (and Save) An Environment of Programs Programming Strategies The Programming Process. 4. Sequences and Strings Representing Sequence Data A Program to Store a DNA Sequence Concatenating DNA Fragments Transcription: DNA to RNA Using the Perl Documentation Calculating the Reverse Complement in Perl Proteins, Files, and Arrays Reading Proteins in Files Arrays Scalar and List Context Exercises. 5. Motifs and Loops Flow Control Code Layout Finding Motifs Counting Nucleotides Exploding Strings into Arrays Operating on Strings Writing to Files Exercises. 6. Subroutines and Bugs Sbroutines Scoping and Subroutines Command-Line Arguments and Arrays Passing Data to Subroutines Modules and Libraries of Subroutines Fixing Bugs in Your Code Exercises. 7. Mutations and Randomization Random Number Generators A Program Using Randomization A Program to Simulate DNA Mutation Generating Random DNA Analyzing DNA Exercises. 8. The Genetic Code Hashes Data Structures and Algorithms for Biology The Genetic Code Translating DNA into Proteins Reading DNA from Files in FASTA Format Reading Frames Exercises. 9. Restriction Maps and Regular Expressions Regular Expressions Restriction Maps and Restriction Enzymes Perl Operations Exercises. 10. GenBank GenBank Files GenBank Libraries Separating Sequence and Annotation Parsing Annotations Indexing GenBank with DBM Exercises. 11. Protein Data Bank Files and Folders PDB Files Parsing PDB Files Controlling Other Programs Exercises 12. BLAST Obtaining BLAST String Matching and Homology BLAST Output Files Parsing BLAST Output Presenting Data Bioperl Exercises. 13. Further Topics The Art of Program Design Web Programming Algorithms and Sequence Alignment Object-Oriented Programming Perl Modules Complex Data Structures Relational Databases Microarrays and XML Graphics Programming Modeling Networks DNA Computers A. Resources B. Perl Summary Index

About the Author

James Tisdall has worked as a musician, as a programmer at Bell Labs (where he programmed for speech research and discovered a formal language for musical rhythm), at the Human Genome Project in the Computational Biology and Informatics Laboratory (where he began using Perl for bioinformatics in 1991), at Mercator Genetics in Menlo Park, California, and most recently at the Fox Chase Cancer Center in Philadelphia. He has a BA in mathematics from the City College of New York; an MS in computer science from Columbia University; and is working towards a Ph.D. in computer science at the University of Pennsylvania. In his spare time Jim teaches computer music at the Settlement Music School in Philadelphia.

Ask a Question About this Product More...
Write your question below:
Look for similar items by category
Home » Books » Computers » Programming » Perl
Home » Books » Computers » Programming » CGI
Home » Books » Science » Biology » General
How Fishpond Works
Fishpond works with suppliers all over the world to bring you a huge selection of products, really great prices, and delivery included on over 25 million products that we sell. We do our best every day to make Fishpond an awesome place for customers to shop and get what they want — all at the best prices online.
Webmasters, Bloggers & Website Owners
You can earn a 5% commission by selling Beginning Perl for Bioinformatics on your website. It's easy to get started - we will give you example code. After you're set-up, your website can earn you money while you work, play or even sleep! You should start right now!
Authors / Publishers
Are you the Author or Publisher of a book? Or the manufacturer of one of the millions of products that we sell. You can improve sales and grow your revenue by submitting additional information on this title. The better the information we have about a product, the more we will sell!
Item ships from and is sold by Fishpond World Ltd.
Back to top