CSE 666 Bioinformatics

Fall 2000

Instructor: Dr. Raj Acharya Email: acharya@cse.buffalo.edu Office: 226 Bell Hall Office Hours: To be announced Class newsgroup: sunyab.cse.666

NOTE:
New references have been added in the "Reading Materials" section (Dated : 09/26/2000).

Course Overview:

The study and practice of Molecular Biology is undergoing a revolution. Recently, massive amounts of data (DNA sequences, protein sequences, etc.) are being generated at a rapid rate. Computational Methods play a fundamental role in transforming this massive data sets into meaningful information, resulting in new theories. Bioinformatics is an exciting area that involves developing Computational, Information Theoretic and Mathematical methods for managing and analyzing information about the sequence, structure and function of biological molecules and systems. In this course, we will aim to understand some of the fundamental Computational, Modeling and Information Theoretic problems in molecular biology. We will also be studying a comprehensive and representative subset of widely used algorithms in Computational Molecular Biology.

Prerequisites:

CSE Graduate Standing. Others should obtain permission of instructor. Mathematical maturity as expected of CSE Graduate students is assumed.

Course Contents

The material for the course will cover the basic concepts of topics such as :

Molecular Biology
Pair wise Sequence Alignment
Learning Theory
Data Mining
Hidden Markov Models
Sequence Motifs
Multiple Sequence Alignments
Finding Genes in Genomic DNA
Gene Expression Data and Molecular Medicine
Phylogenetic Trees
Protein Structure Prediction
Fractal Models
Computing with the DNA

Evaluation

Based on Class Presentation & Discussions, Reports, Project.

Reading Materials:

New Reference (Dated: 09/26/2000): Please click here for some additional references.

Primer on molecular genetics: http://www.ornl.gov/hgmis/publicat/primer/prim1.html
New goals for the human genome project: http://www.sciencemag.org/cgi/content/full/282/5389/682

Some Interesting Sites:

Bioinformatics Jump Page: http://bozeman.mbt.washington.edu/bioinformatics.html
Genbank: http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html
SWISS-PROT: http://www.expasy.ch/sprot/
Protein Data Bank: http://www.rcsb.org/pdb/
PROSITE database: http://www.expasy.ch/prosite/
Blocks database: http://www.blocks.fhcrc.org/
MEME server: http://meme.sdsc.edu/meme/website/
Multiple Alignment Servers: http://merlin.mbcr.bcm.tmc.edu:8001/bcd/Curric/MulAli/welcome.html
SAM HMM code: http://www.cse.ucsc.edu/research/compbio/sam.html
HMMER HMM code: http://hmmer.wustl.edu/
PFAM database of multiple alignments: http://pfam.wustl.edu/
GRAIL server: http://compbio.ornl.gov/Grail-1.3/
ORNL Computational Bioscience Center: http://compbio.ornl.gov/
Gene recognition bibliography: http://linkage.rockefeller.edu/wli/gene/
Molecular pattern recognition: http://www.genome.wi.mit.edu/MPR/
Genome wide expression patterns: http://rana.Stanford.EDU/clustering/
Support vector machine: http://www-ai.cs.uni-dortmund.de/SOFTWARE/SVM_LIGHT/svm_light.eng.html
Secondary structure data set: ftp://ftp.ics.uci.edu/pub/machine-learning-databases/molecular- biology/protein-secondary-structure/
DNA Junk Noise is Fractal: http://www.scitec.auckland.ac.nz/~king/Preprints/book/evol/ noisy/junk.htm

Academic Integrity

The department has not witnessed any cases of plagiarism in the past and hopes that the trend continues in the future too. The departmental policy on Academic Integrity is reproduced below for your convenience:

As a good rule of thumb, you may discuss any problem in the course as long as no one is using a writing implement (computers included) nor looking at any source code for the assignment. That is, any group work must be verbal only. Obviously you may look at the textbook or class handouts/class notes together. One exception to this rule is that when a friend is having trouble with a small bug, and you notice a typo or other "silly little mistake", you may point it out to them. More substantive assistance is definitely not allowed, from any source whatsoever, including tutors or friends not enrolled in the course. The professor or teaching assistants will be able to give more help if you are stuck with concepts.

All academic work must be your own. Collaboration, usually evidenced by unjustifiable similarity in assignments, is never allowed. After an appropriate informal review, if any students are found in violation of maintaining academic integrity, sanctions will be imposed, which can be as severe as receiving an F in the course. Especially flagrant violations will be considered under formal review proceedings, which can call for harsher sanctions including expulsion from the University. If you ever have any questions or concerns regarding the policy, particularly as it relates to this course, see your instructor.