Large Scale Biological Sequence Analysis

and Visualization

Ed H. Chi

Apprentice, The Geometry Center

Graudate Student, Univeristy of Minnesota, CSci Dept.

Welcome!

1. What is Computational Molecular Biology?

2. The need to Analyze Genetic Information

3. The tools behind our Analysis: Genome Database & Similarity Algorithms

4. The powerfulness of Visualization

What is Computational Molecular Biology?

Primer on Molecular Genetics

DNA story

DNA structure

DNA replication

Gene Expression

Down's Syndrome

Cloning using plasmids

Overlapping Clone library

Sequencing Technology

Genome Size

Size of genome data

The Holy Grail of Molecular Biology

The need to Analyze Genetic data

The need to understand functions of certain proteins to treat disease, find antibodies, etc, leds us to find means to interpret the data

Diabetics, Lesch-Nyhan Syndrome (a buildup of uric acid wastes), Cancer

show mice chromosome maps

show human chromosome maps

THE DATABASES:

GenBank

PIR, Swissprot, GenPept

EC-Enzyme

Mapping Databases (GDB) at Johns Hopkins University

OUR ANALYSIS SYSTEM: Arabidopsis Large Scale Sequence Analysis Project

Pictures and gels of Arabidopsis from AAtDB WWW home page.

Arabidopsis Analysis System GIF

SIMILARITY ALGORITHMS:

Example of our HTML result file for the analysis

BLAST result report

Explain PAM matrix: evolutionary distance

Generalized Suffix Trees for Biological Sequences

Example problem:

recognizing Low Complexity Regions:

intrinsic repeats and repetitive elements

Johns Hopkins University BioInformatics

Show 3D protein structure examples

Other 3D protein sturcture examples

My Visualization Software

1. 1G5T7P.STD : another simple example

2. SCC12T7P.STD : a simple example

3. 37C5T7.STD : example of filtering

4. 11B11T7P.STD : example of conserved regions & filtering

1. some understanding of computational molecular biology (WHAT)

2. the need to understand biological sequences (WHY)

3. some knowledge of what tools are used and could be used (HOW)

QUESTIONS?

Sounds of Bird calls