60-558 Winter 2008
Computational Molecular Biology

Some materials provided by courtesy of Dr. Serafim Batzoglou.

• Lecture 01: Introduction to Computational Molecular Biology
• Lecture 02: Introduction to Biology
• Lecture 03: Pairwise Sequence Alignment Algorithms
• Lecture 04: Efficient Pairwise Alignment Algorithms
• Lecture 05: Hidden Markov Models
• Lecture 06: Variants of Hidden Markov Models
• Lecture 07: Hidden Markov Modeling Example
• Lecture 08: Pair Hidden Markov Models
• Lecture 09: DNA Sequencing
• Lecture 10: Hierarchical DNA Sequencing
• Lecture 11: Molecular Evolution and Phylogenetic Tree Reconstruction
• Lecture 12: DNA Fragment Assembly
• Lecture 13: Multiple Sequence Alignment Algorithms I
• Lecture 14: Multiple Sequence Alignment Algorithms II
• Lecture 15: Rapid Global Alignments
• Lecture 16: Gene Recognition
• Lecture 17: Gene Recognition

• Introduction 2006, Introduction 2008
• Pairwise Sequence Alignments 2006, Pairwise Sequence Alignments 2008
• Lecture 3: Multiple Sequence Alignment
• Lecture 4: Fasta, Blast, and Probabilities
• Lecture 5: Markov Chains
• Lecture 6: Hidden Markov Models (Short) Hidden Markov Models (Long) Hidden Markov Models (Learning)
• Lecture 5: Perl Slides and Examples.
• Lecture 6: CMB11.ppt, CMB03c.pdf, CMB04c.pdf.
• Lecture 7: Blec05.pdf, CMB13.pdf, CMB14.ppt, CMB15.ppt.
• Lecture 8: Blec02.pdf, CMB17.ppt.

· Assignments

• Assignment 1 (The last section of the assignment is a bonus question.)
• Assignment 2 (new)

· Other Materials

• BioPerl: http://bio.perl.org or http://bioperl.org
• Perl: http://www.perl.com
• BioPerl Tutorial: http://www.bioperl.org/Core/Latest/bptutorial.html
• BioPerl Course: http://www.pasteur.fr/recherche/unites/sis/formation/bioperl/
• BioJava: http://biojava.org/
• BioJava Tutorial: http://www.biojava.org/tutorial.html