Tutorial Title: Soft Computing in Bioinformatics

This tutorial will go over the basics of creating and using similarities between gene products, i.e., proteins or mRNA.  We discuss the various categories of similarity measures beginning with the traditional BLAST scores on gene product sequences and culminating with recent research results in the application of fuzzy set theory to this problem.  Clustering, knowledge discovery and applications to microarray experiments will be stressed.  The following is a topical outline:

 I.  Background
            Genes and Gene Products
                        Sequences
                        Structure
                        Microarrays (expression, hypermethylation)
            Gene Ontology
            Other taxonomies
II.  Gene Product Similarity Measures
            BLAST
            Smith-Waterman
            GO-based measures
                        Jaccard, Cosine, Dice
                        Fuzzy measures
                        Choquet Integrals
            Domain and Motif measures
III.  Visualization and Clustering
            Hierarchical clustering
            Visual Assessment of cluster Tendency
            NERFCM
IV.  Knowledge Discovery
V.  Function Summarization