Application of Commercial and Web-Based Software Programs for DNA Sequence Analysis in Undergraduate Biochemistry Laboratory

TCE

The Chemical Educator

ISSN: 1430-4171 (electronic version)

Table of Contents

Abstract Volume 10 Issue 3 (2005) pp 186-189

Application of Commercial and Web-Based Software Programs for DNA Sequence Analysis in Undergraduate Biochemistry Laboratory

Beng Guat Ooi

Department of Chemistry, Middle Tennessee State University, Murfreesboro, TN 37132, bgooi@mtsu.edu
Received September 8, 2004. Accepted January 29, 2005.

Published online: 15 April 2005

Abstract. The purpose of this laboratory experiment is to teach undergraduate students how to use a commercial software program and Internet resources to analyze DNA sequences. Several primers were designed for DNA sequencing of the xylose reductase gene so that students can learn to reconstruct the gene sequence by linking and aligning fragmented sequences with the help of DNASTAR’s Lasergene software. This program will also allow students to determine the start and termination of the gene sequence, edit and annotate the sequence, and present the DNA sequence in the widely used GenBank format. Students will learn the procedures for comparing their sequences with published DNA data available via the Internet and determining the exact sizes of the amplified fragments by mapping the locations of the primers that are used for making the PCR fragments.

Key Words: Computers in Chemistry; biochemistry

(*) Corresponding author. (E-mail: bgooi@mtsu.edu)

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Supporting Materials:

Files containing the prelaboratory exercise and laboratory instructions for students and the unprocessed fragmented sequences of C. tropicalis can be downloaded as supporting materials by instructors planning to use this experimental procedure. (152 KB Zip file)