The Central Dogma
DNA and RNA
Chromosomes
Proteins
The Central Dogma
Transcription and Translation in Perl
RNA Secondary Structure
Messenger and Catalytic RNA
Levels of RNA Structure
Constraints on Secondary Structure
RNA Secondary Structures in Perl
Counting Hydrogen Bonds
Folding RNA
Comparing DNA Sequences
DNA Sequencing and Sequence Assembly
Alignments and Similarity
Alignment and Similarity in Perl
Predicting Species: Statistical Models
Perl Subroutine Libraries
Species Prediction in Perl
Substitution Matrices for Amino Acids
More on Homology
Deriving Substitution Matrices from Alignments
Substitution Matrices in Perl
The PAM Matrices
PAM Matrices in Perl
Sequence Databases
FASTA Format
GenBank Format
GenBank's Feature Locations
Reading Sequence Files in Perl
Object-Oriented Programming in Perl
The SimpleReader Class
Hiding File Formats with Method Inheritance
Local Alignment and the BLAST Heuristic
The Smith-Waterman Algorithm
The BLAST Heuristic
Preprocessing the Query String
Scanning the Target String
Implementing BLAST in Perl
Statistics of BLAST Database Searches
BLAST Scores for Random DNA
BLAST Scores for Random Residues
BLAST Statistics in Perl
Interpreting BLAST Output
Multiple Sequence Alignment I
Extending the Needleman-Wunsch Algorithm
NP-Completeness
Alignment Merging: A Building Block for Heuristics
Merging Alignments in Perl
Finding a Good Merge Order.