Wright State University

Source Code for Perl Examples in Appendix 3 of Krane & Raymer

• Example 1: Conceptual Translation
• Example 2: Dot Plot
• Example 3: Relative Rate Test
• Example 4: UPGMA
• Example 5: Common Ancestor Analysis
• Example 6: Splice Junctions
• Example 7: Simple Lattice Models
• Example 8: Atomic Density
• Example 9: Linear Regression

Misc. Perl Code Skeletons

Section 1: Scalar Variables and Basic Perl

• Example 0: Printing in Perl
• Example 1: Scalar Variables
• Example 2: Using STDIN
• Example 3: Scalar Operators
• Practice Problem 1: Printing a Codon
• Solution to Practice Problem 1
• Example 4: Pragmas

Section 2: Conditionals, Logical Operations, and Flow Control

• Example 0: Logical Operators
• Example 1: Error Checking
• Example 2: While Loops
• Practice Problem 2: Counting Nucleotides
• Solution to Problem 2: Counting Nucleotides

Section 3: List Variables and Operators

• Example 0: Lists
• Example 1: Input files
• Example 2: Counting Nucleotides Again
• Example 3: Using Split()
• Practice Problem 3: DotPlot
• Solution to Problem 3: DotPlot

Section 4: Regular Expressions in Perl

• Example 0: Recognizing Motifs

Sequence Data for Practice

• Single line gene sequence
• Multi-line gene sequence

Examples of Lab Assignments

• Lab Assignment: Conceptual Translation (PDF)
• Lab Assignment: Models of Substitution

Miscellany

• IEEE Transactions on Education Manuscript

This material is based upon work supported by the National Science Foundation under award #EIA-0122582. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.