Perl Developer - Cessnock

BioPerl Module

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
3. 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
4. Motifs and Loops
•Flow Control
•Code Layout
•Finding Motifs
•Counting Nucleotides
•Exploding Strings into Arrays
•Operating on Strings
5. Subroutines and Bugs
•Subroutines
•Scoping and Subroutines
•Command-Line Arguments and Arrays
•Passing Data to Subroutines
•Modules and Libraries of Subroutines
•Fixing Bugs in Your Code
6. Mutations and Randomization
•Random Number Generators
•A Program Using Randomization
•A Program to Simulate DNA Mutation
•Generating Random DNA
•Analyzing DNA
7. 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
8. Restriction Maps and Regular Expressions
•Regular Expressions
•Restriction Maps and Restriction Enzymes
•Perl Operations
9. Protein Data Bank
•Overview of PDB
•Files and Folders
•PDB Files
•Parsing PDB Files
•Controlling Other Programs
10. BLAST
•Obtaining BLAST
•String Matching and HomologyIT-SC
•BLAST Output Files
•Parsing BLAST Output
•Presenting Data
•Bioperl