Medical Information Sciences 214 (also listed as Computer Science 274)

Representations and Algorithms for Computational Molecular Biology

Time: Tues/Thurs 1:15-2:30

Location: Gates Building, Room B01

Videotape: Available at Math/CS Library

Internet:  Course offered over Stanford Online

Schedule of Lectures (HTML table)

Assignments and Projects in PDF format

• Assignment 0 (DUE APRIL 2): Student Survey
• Assignment 1 (DUE APRIL 7)
• Protein Data Bank
• The National Center for Biotechnology Information (NCBI)
• Swiss-Prot
• Other Resources

 
• Project 1 (DUE APRIL 21): Dynamic Programming for Sequence Alignment
• Instructions (PDF format)
• Three hardcopy papers distributed in class (see coordinator for copies)
• align-example.input, align-example.input-annotated, align-example.output, align-all-example.output

align1.dat, align2.dat, align3-template.dat,   p1.sequences
• Assignment 2 (DUE APRIL 28)
• Test sequence and database
• FTP directory with working SUN binary for sequence alignment
• Assignment 3 (DUE MAY 7)
• Protein Data Bank
• FTP site for MAGE for MAC
• FTP site for MAGE for PC
• FTP site for MAGE for UNIX
• Another MAGE Program download site for Mac and PC/Windows, Alternative MAGE Program download site for many platforms.
• Project 2 (DUE MAY 19): Computing distances and dihedral angles
• 2TIR.DAT
• Assignment 4 (DUE MAY 28) Fold Recognition with Environments
• FTP directory to working dynamic programming algorithm
• Input files align.thread, align.standard, and a4.dat
• For background, see also Bowie, Luthy & Eisenberg, SCIENCE 253, p. 164-170, July 12, 1991
• Project 3 (DUE JUNE 6) RMS Fitting of 3D Structures
• Instructions (PDF)
• FTP directory with code for SVD
• Alpha-carbon coordinates for 1MBD and 4HHB_A
• See also IEEE paper by Arun et al.
• Assignment 5 (DUE JUNE 6) Course Evaluation, required

 

• March 31 (ALTMAN): Introduction to Bioinformatics
• DNA kinemage
• Protein backbone kinemage
• Betasheet kinemage
• Basic biology primer.
• Basic chemical bonding primer
• Protein Architecture
• Introduction to DNA structure
• Introduction to Genetics
• Glossary of Genetic Terms
• Overview of Human Genome Project goals
• April 2 (KOZA): Introduction to structure
• Week 1 Suggested Readings
• April 7 (ALTMAN):  Dynamic Programming for Sequence Alignment
• April 9 (ALTMAN):  (Addendum on Sequence Alignment) Basic Structural Computations
• Color slides
• 3 per page
• The Library of Protein Family Cores (LPFC)
• Dr. Gerstein's lecture on surface and volume computations
• The WAC substitution matrix
• Amino acid substitution matrices from an information theoretic perspective
• Methods for assessing the statistical significance of alignments
• April 14 (ALTMAN):  Protein folding, energy minimization and dynamics
• Color slides of the lecture
• Black and White slides, 3 per page.
• Recent review of protein folding
• Lattice models of proteins
• Molecular dynamics MPEGS shown in class:  overview & detail
• April 16 (ALTMAN):  Protein structure prediction:  homology modeling, ab initio and threading
• Color slides of the lecture
• Black and white slides, 3 per page.
• Protein Prediction Center
• April 21 (ALTMAN):  Sequence motifs:  definition and computation
• Color slides of the lecture
• Black and white slides, 3 per page
• Useful refereces to motifs
• Prosite Database
• EMOTIF server
• MEME resource
• Blocks Database
• Sequence logo graphics
• April 23 (ALTMAN/SCHMIDLER):  Multiple Alignment and Hidden Markov Models
• Brief introduction, color slides
• Brief introduction, 3 per page
• Hidden Markov Models, color slides
• Hidden Markov Models, 3 per page
• Useful web references for multiple alignment
• UC Santa Cruz HMM applications and tools
• Washington University, St. Louis HMM tools
• April 28 (SCHMIDLER) Protein Secondary Structure Prediction
• Color slides
• 3 per page
• SSP Server
• PhD Server:
• Other servers
• Other links of relevance
• April 30 (ALTMAN) Computing With Distances
• Color slides
• 3 per page
• May 5 (ALTMAN and WEI) Non Atomic Representations of Molecular Structure: 3D Motifs
• Color slides
• 3 per page
• Description of basic 3D motif techniques
• 3D motifs used for creating a sequence alignment match matrix
• 3D motifs used for recognizing sites in proteins
• 3D motifs used to compare amino acid environments
• May 7 (ALTMAN) Structural Alignment
• Color slides
• 3 per page
• DALI server
• LOCK server
• May 12 (ALTMAN) Evolutionary Trees
• Color slides
• 3 per page
• American Natural History page on vertebrate development
• Treebase database of phylogenetic information for plants mostly
• Tree of Life Page
• Samples from the Tree of Life
• Ribosomal Database Project
• MaClade program for analyzing character based trees
• Other notes on phylogenetic tree construction
• Phylip package for phylogenetic analysis
• May 14 (ALTMAN) Integrating Heterogeneous Biological Databases
• Color slides
• 3 per page
• Introduction to OPM system for integrating biological databases
• Introduction to Kleisli system for integrating biological databases
• Meeting on the Interconnection of Molecular Biology Databases
• Sample BioKleisli usage: finding important unknown protein structures
• DBGET
• ENTREZ
• SRS
• GDB example of OPM
• BioKleisli examples
• May 19 (ALTMAN) Collaborative Environments for Biology
• Color slides
• 3 per page
• The BioMOO
• The Worm Community System
• The Cell Signaling Networks database
• The Ion Channel Network
• Biology Workbench
• The RiboWEB Knowledge Base
• May 21 (KOZA) Genetic Algorithms and Genetic Programming
• Full page slides
• 4 per page
• May 26 (KARP) Metabolic Databases
• EcoCyc home page
• Pathway Databases
• May 28 (KOZA) Genetic Algorithms and Genetic Programming - Addendum
• Full page slides
• 4 per page
• June 2 (ALTMAN) RNA Structure Computations
• Color slides
• 3 per page
• The RNA World
• Michael Zuker's RNA Folding Server

Other Links (in PDF format unless otherwise noted)

• Dynamic programming algorithm on the web
• FTP site for MAGE for MAC
• FTP site for MAGE for PC
• FTP site for MAGE for UNIX
• Another MAGE Program download site for Mac and PC/Windows, Alternative MAGE Program download site for many platforms.
• Macintosh GENEWORKS demo software
• RasMol display program for molecules. Tutorial on using it with some proteins.
• SCOP resource for defining protein families.
• The EcoCYC browser
• The various resources at San Diego Supercomputer Center including: MOOSE, Protein Kinase Specialty Data Collection , Fast topology search, Exact structure pair matching , Introduction to mmCIF, and Introduction to all relevant software to course .
• Lecture notes on Computing molecular surfaces and volumes,
• Protein Motions Database
• The link to genome databases at Stanford.

General Course Information

Russ Altman, Assistant Professor of Medicine (and Computer Science, by courtesy), Stanford Medical Informatics. MSOB X-215, Stanford, Mail Code 5479. 650-725-3394, altman@smi.stanford.edu

John Koza, Consulting Professor of Computer Science and Symbolic Systems, Gates Building 258, Stanford, Mail Code 9020, 650-723-1517, koza@cs.stanford.edu
 

Teaching Assistant:

Scott Schmidler, scs@smi.stanford.edu, 650-723-2990
Office Hours to be determined.

Course Coordinator: Kevin Lauderdale, MSOB X215, (650) 725-0659, kxl@smi.stanford.edu

Description:

This course will introduce the basic computational issues and methods used in molecular biology, combining core lectures, programming assignments, and guest lectures. In addition, the course will introduce and use biological data sources available on the world wide web media. Topics will include basic algorithms for alignment of biological sequences and structures, as well as more advanced representational and algorithmic issues in structure and sequence computation. These include, for example, dynamic programming algorithms for alignment, structural superposition algorithms, simplified representations, probabilistic representations of structural uncertainty, hidden Markov models, Bayesian networks, statistical feature detection, genetic algorithms, constraint satisfaction and minimum description length encoding. The guest lectures will, in part, showcase different computational approaches being pursued by different research groups in several departments at Stanford.

We will assume no previous biology background. We will assume an interest in biology, however.

Units:

• This course is normally taken for 4 units.
• It can be taken for 3 units by arrangement with instructors.
• A lecture-only, no assignment participation may be taken for 1 unit by arrangement with instructors.
• Finally, this course is offered jointly with MIS 212, A project-building course.  The two courses can be taken together for 5 units.

Auditors: Must be approved by Dr. Altman.

Prerequisites: Matrix mathematics and programming skills required. Familiarity with biology helpful, but not required. The CS requirement is meant to ensure that people can write computer programs, and understand the basics of data structures and algorithms. The math requirement is meant to ensure that people feel comfortable with matrix algebra.

Computer resources: You will need to have access to email on the internet. In particular, we will use a WWW browser (forms-compatible), such as Netscape. All of these resources are available to Stanford students at Sweet Hall and elsewhere. All course material will be placed on the WWW in *.pdf (Adobe Acrobat) format, which allows the documents to be read on multiple platforms. Readers are available for free for Windows, Macintosh and many unix platforms at the Adobe website.

Course readings: Will be distributed as needed in class, or through the course coordinator. Assignments and Projects will be made available electronically only.