Teaching material in "alignment/database-search" module.

Single sequence alignments

• Biological motivation
• Introduction
• Pairwise alignments
• Dynamic programming
• Substitution matrices
• Using alignments to search databases.

Blast Fasta and E-values

• Statistics of sequence alignments.
• Heuristic methods
• Implementations

Multiple sequence alignments

• Multiple sequence alignments
• Profiles
• PSIBLAST
• clustalW
• Hidden Markov Models

Assignment pages

• Aligning 2 proteins
• Blast/fasta/psiblast (non-www)
• ClustalW and HMM (non-www)

The content of some of these pages was stolen from http://www.psc.edu/biomed/dist-ed/ and http://www.ncbi.nlm.nih.gov/BLAST/tutorial/