Biology 419

BIOL 419
Introduction to Molecular Bioinformatics

Catalog Entry

Biology 419. Introduction to Molecular Bioinformatics
Three hours lecture. (3).

Prerequisites: A grade of "C" or better in either STAT 219 or STAT 200 and a grade of "C" or better in either BIOL 131, BIOL 132, BIOL 231, BIOL 232 and CHEM 102; or BIOL/CHEM  471/472; or permission of the instructor

This course will provide a broad introduction to the area of bioinformatics.  Topics include: molecular biology background, protein structure and function, sequence alignment algorithms, protein structure prediction, structure-structure alignment, public sequence/structure databases and search tools, introductory phylogenetic analysis, and introduction to systems biology.


Detailed Description of Content of the Course

This is a general introduction to bioinformatics with an emphasis on use of available public databases and computer software to address molecular biological questions.  Emphasis of the class will follow existing trends and tools available but will most likely always cover the following concepts and applications.  Emphasis will be placed on familiarization with tools and databases through problem solving.

Bioinformatics Databases:

Sequence and sequence alignment formats, data exchange.

Public sequence databases.

Sequence retrieval

Public protein structure databases.

Sequence database search tools.

Structure database search tools.

Gene expression databases

Physical and Chemical properties of nucleic acids.

RNA-folding and structure prediction.


Physical and Chemical properties of proteins.

Prediction of protein secondary structure.

Protein domains and prediction of domain boundaries.

Protein structure-function relationships

Protein folding

Prediction of functionally important sites.

Structure-structure alignment algorithms.

Protein structure classification.

Sequence Alignment

Pairwise sequence alignment algorithms.

Multiple sequence alignment algorithms.

Sequence profiles and profile alignment.

Alignment statistics.

Assessment of genetic variation and experimental techniques.

The HapMap project.

Human genetic variation.

Sequencing, PCR.

Microarrays and gene expression.

Phylogenetic Analysis

Molecular basis of evolution.

Taxonomy and phylogenetics.

Phylogenetic trees and phylogenetic inference.

Software tools for phylogenetic analysis.

Accuracies and statistical tests of phylogenetic trees.

Genome comparisons.

Protein structure evolution.

Gene identification.

Genome analysis.

The laboratory portion of this course will be strictly computer oriented.  No additional laboratory equipment or budget is necessary.  These needs can be met with the existing computer labs on campus.


Detailed Description of Conduct of the Course

This will be a problems based course supplemented with lecture, discussion and oral presentation of group projects.   Individual homework may be assigned to familiarize students with the databases/applications being covered.  Group research projects will emphasize each unit of material.  Field trips may be incorporated into the course when appropriate.


Goals and Objectives of the Course

The ability to access and search Bioinformatics databases is now a key component of most biological research. This course will provide an overview of the nature of Bioinformatics databases and the techniques used to access them. Students will be taught practical skills in searching key databases such as Genbank and SwissProt, and interpreting the results. They will also be introduced to more specialized databases such as Kegg and to the use of tools such as Clustal, SwissModel, and Blast for sequence alignment and protein modeling.  Upon completion of this course students will:


·         have a broad overview of bioinformatics.

·         have a familiarity with basic computer concepts and their everyday use in a biological laboratory setting.

·         Be acquainted with the structure of molecular sequence databases and with the methods to analyze their contents.

·         Be able to navigate the more broadly used biological resources available on the Internet.

·         Be able to describe the possibilities and limitations of computer-assisted analysis of sequence and genomic data.

·         be able to interpret the results of bioinformatics database searches 

The course focuses on practical problems using computers.


Assessment Measures

Students will be assessed by their performance on exams and homework assignments, their participation on group projects and by performance on in-class presentations.


Other Course Information


Review and Approval

October, 2007

Revised    4/13/09    Gary Coté