About this book
Complements the excellent Developing Bioinformatics Skills as a practical guide on using the Perl programming language for processing biological data. With comprehensive tutorial chapters, Tisdall provides a solid grounding in Perl language and techniques, before examining detailed case studies such as Genbank and BLAST. The text rounds off with useful appendices covering relevant resources and a Perl language summary.
Ideal for those engaged in natural sciences data processing and in fact an excellent primer for anyone considering Perl programming.
&b;Biology and Computer Science:&o; The Organization of DNA; The Organization of Protein; In Silico; Limits to Computation.
&b;Getting Started with Perl:&o; A Low and Long Learning Curve; Perl's Benefits; Installing Perl on Your Computer; How to Run Perl Programs; Text Editors; Finding Help.
&b; The Art of Programming:&o; Individual Approaches to Programming: Edit-Run-Revise (and Save): An Environment of Programs; Programming Strategies; The Programming Process.
&b; Sequences and Strings:&o; 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.
&b; Motifs and Loops:&o; Flow Control; Code Layout; Finding Motifs; Counting Nucleotides; Exploding Strings into Arrays; Operating on Strings; Writing to Files; Exercises.
&b; Subroutines and Bugs:&o; Subroutines; Scoping and Subroutines; Command-Line Arguments and Arrays; Passing Data to Subroutines; Modules and Libraries of Subroutines; Fixing Bugs in Your Code; Exercises.
&b; Mutations and Randomization:&o; Random Number Generators; A Program Using Randomization; A Program to Simulate DNA Mutation; Generating Random DNA; Analyzing DNA; Exercises.
&b; The Genetic Code:&o; Hashes; Data Structures and Algorithms for Biology; The Genetic Code; Translating DNA into Proteins; Reading DNA from Files in FASTA Format; Reading Frames; Exercises.
&b; Restriction Maps and Regular Expressions:&o; Regular Expressions; Restriction Maps and Restriction Enzymes; Perl Operations; Exercises.
&b; GenBank: &o; GenBank Files; GenBank Libraries; Separating Sequence and Annotation; Parsing Annotations; Indexing GenBank with DBM; Exercises.
&b; Protein Data Bank:&o; Files and Folders; PDB Files; Parsing PDB Files; Controlling Other Programs; Exercises.
&b; BLAST:&o; Obtaining BLAST; String Matching and Homology; BLAST Output Files; Parsing BLAST Output; Presenting Data; Bioperl; Exercises.
&b; Further Topics:&o; 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.
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.