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Bioinformatics

By Monica Bruckner, Montana State University; Based on the Bioinformatics Exercise by Seth Bordenstein.
This material was originally developed through Microbial Life Educational Resources
as part of its collaboration with the SERC Pedagogic Service.

Summary

This exercise contains two interrelated modules that introduce students to modern biological techniques in the area of Bioinformatics, which is the application of computer technology to the management of biological information. The need for Bioinformatics has arisen from the recent explosion of publicly available genomic information, such as that resulting from the Human Genome Project.

Learning Goals

By the end of this activity, students will:
  • Be exposed to the tools and databases currently used by researchers in molecular and evolutionary biology;
  • Gain a better understanding of gene analysis, taxonomy, and evolution.

Context for Use

Part or all of this activity can be used in an introductory microbiology or genetics course. This activity is based on the Bioinformatics Exercise, part of Microbial Life Educational Resources. While no computer programming skills are necessary to complete the modules in this work, prior exposure to personal computers and the Internet will be assumed. The main program that you will need is an Internet browser, such as Netscape Navigator or Internet Explorer.

Teaching Materials

This exercise represents a series of interrelated modules designed to introduce the student to modern biological techniques in the area of Bioinformatics. Bioinformatics is the application of computer technology to the management of biological information. The need for Bioinformatics has arisen from the recent explosion of publicly available genomic information, such as that resulting from the Human Genome Project. To address this, the National Center for Biotechnology Information (NCBI) was established in 1988 as a national resource for molecular biology information. The NCBI creates public-access databases, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease. The NCBI is a virtual goldmine both in terms of available resources, and treasures yet to be discovered. Some of the many databases that the NCBI is responsible for include the GenBank DNA sequence database, containing millions of nucleotide sequence records; the Molecular Modeling Database (MMDB) consisting of three-dimensional protein structures, as well as tools for their visualization and comparative analysis; and the Online Mendelian Inheritance in Man (OMIM) database, which is a catalog of human genes and genetic disorders.

This activity is based on the Bioinformatics Exercise, part of Microbial Life Educational Resources. The activity contains two modules, which may be used independently or as a whole, depending on course content and/or time constraints. These modules include:

PCR machines

Module 1: Sequence Taxonomy: This module will introduce you to the number and diversity of sequences in the NCBI database.

Nasonia vitripennis female using her ovipositor to lay her eggs inside the host fly pupa

Module 2: Sequence Searching and BLAST: This module will show you how to retrieve genetic sequence data from the NCBI database that identifies a particular Wolbachia sequence.

The links to each module (above) include material and information needed to complete this activity (e.g. background information links to databases, and problem sets specific to each module).

Teaching Notes and Tips

This activity can be used as a lab or as a homework assignment. It takes students approximately 1 hr to complete. Introducing basic ideas in class before the assignment is important to help students get started. Students' questions related to the completion of this activity help build student interest in classroom discussion.

Assessment

The successful completion of this activity and evaluation of students' results are good measures of student comprehension. Follow-up discussions in class, essay questions on exams, and the future success of students on other related activities are also useful measures of student understanding.

References and Resources

This activity is based on the Bioinformatics Exercise, part of the Microbial Life Educational Resources Project.

Download (Microsoft Word 65kB Jul26 07) this exercise as a Word document.

There are a number of online, educational resources devoted to learning bioinformatics. For details that summarize what we will cover in this exercise and more, see: