Specific Programs
BLAST The NCBI's introduction to using BLAST
BLAST Another tutorial on BLAST from The Institute for Cancer Research
RasMol A tutorial on RasMol from The Institute for Cancer Research
DOE Primer The DOE's excellent Primer on Molecular Genetics
Sequence Alignment and Searching
Algorithm Primer Paracel's introduction to similarity searching algorithms (BLAST, FASTA, Smith-Waterman, HMMs and other profile methods)
DKfz Lectures An excellent set of online lectures on sequence alignment, database searching and phylogeny from the Theoretical Bioinformatics department of the German Cancer Research Institute
Multiple Sequence Alignment A set of slides from Arnaud Sahuguet at the University of Pennsylvania
Protein Structure
Principles of Protein Structure 1997 Birkbeck's MSc course materials from 1997
Mixed Tutorials
MBDC Tutorials Oxford's tutorials on Unix, GCG, Seqlab and Staden
BioComputing Hypertext Coursebook Texas Medical Center's tutorials on sequence alignment, phylogenetics, genetic algorithms and protein folding
Computational Approaches to Protein Structure Emory University's guide to homology searches, multiple alignments, secondary structure prediction, epitope prediction, accessibility prediction, coiled-coil prediction, and motif/domain searching
Bioinformatics and Genomic Analysis Course notes from the University of Arizona
Introduction to Bioinformatics Lectures from the University of Chicago
Dynamic Programming A general tutorial (not bioinformatics specific) from Michael Trick, Carnegie Mellon University