Talk on Large Scale DNA Sequence Analysis and Visualization

Large Scale Biological Sequence Analysis

and Visualization

Ed H. Chi

Apprentice, The Geometry Center

Graudate Student, Univeristy of Minnesota, CSci Dept.

Monday, July 11th, 1994. 3pm


The Messages are:

  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

  1. DNA structure

  2. DNA replication

  3. Gene Expression

  4. Down's Syndrome

  5. Cloning using plasmids

  6. Overlapping Clone library

  7. Sequencing Technology

  8. Genome Size

  9. Size of genome data

  10. 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 TOOLS: Biological Sequence Databases

& Similarity Algorithms



PIR, Swissprot, GenPept


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


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

Visualization in Molecular Biology

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

What I hope you got out of this...

  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)


USA Weather Map

Sounds of Bird calls

Harvard Biological Lab - Genome Research

Human Genome Physical Map Shows examples gel contents