Syllabus

Biomolecular Informatics: Sequence to Structure to Function (BIOC156/MEDC156)
Part of the Methods in Biophysics Series

Instructor: Iosif Vaisman, School of Pharmacy

Spring 2000: Feb 18 - Mar 28, Lec: T 2:30-3:30, F 2:00-3:00; Lab T 3:30-5:00 (2307 McGavran-Greenberg)

Lectures
(Lecture notes will be posted on this page after the lectures)

1. Introduction to information theory	Measures of information Information content of biomolecular sequences Information and Shannon's entropy	html pdf
2. Introduction to computer networks and network-based bioinformatics resources	Internet organization and architecture Distributed computing and server-client information systems Research and collaboration on Internet Electronic publishing Molecular visualization	html pdf
3. Principles of data organization	Databases and database structure Biomolecular databases: DNA and protein sequences, genomes, protein structures Interfaces and data access	pdf
4. Artificial intelligence for biomolecular applications	Stochastic and mechanistic models. Neural networks Genetic algorithms Markov models and hidden Markov models	pdf
5. Sequence alignment and database search algorithms	String alignment problem Scoring functions and substitution matrices Dayhoff and BLOSUM matrices BLAST, FASTA, and Smith-Waterman algorithms	pdf
6. Multiple sequence alignment	String comparison in n dimensions Phylogenetic analysis Multiple sequence alignment algorithms and programs	pdf
7. Secondary structure prediction	Knowledge-based methods for structure prediction Artificial intelligence in structure prediction	pdf
8. Three-dimensional structure	Protein folding problem and its complexity Ab initio methods of protein structure prediction Energy based methods of structure prediction and refinement Homology modeling	pdf
9. Sequence-structure-function correlations	Patterns in protein sequences and structures. Databases of protein sites and motifs	pdf
10. Genome informatics	Recognizable patterns in DNA sequences: promoter regions, exons, introns, start and stop codons Gene identification and prediction Genome mapping Accuracy of gene prediction

Assignments

Exercises
SChiSM exercise: page 1, page 2
Molecular Biology Databases
Algorithms for Sequence Analysis exercise
Protein Modeling exercise
Gene prediction exercise

Instructor: Iosif Vaisman, School of Pharmacy

The development of this course is supported in part by the Education Enhancement Grant from the North Carolina Biotechnology Center