Intrageneric primer design: Bringing bioinformatics tools to the class

Abstract

Bioinformatics is one of the fastest growing scientific areas over the last decade. It focuses on the use of informatics tools for the organization and analysis of biological data. An example of their importance is the availability nowadays of dozens of software programs for genomic and proteomic studies. Thus, there is a growing field (private and academic) with a need for bachelor of science students with bioinformatics skills. In consideration of this need, described here is a problem-based class in which students are asked to design a set of intrageneric primers for PCR. The exercise is divided into five classes of 1 h each, in which students use freeware bioinformatics tools and data bases available through the Internet. Besides designing the set of primers, the students will consequently learn the significance and use of the major bioinformatics procedures, such as searching a data base, conducting and analyzing sequence multialignment, comparing sequences with a data base, and selecting primers. © 2006 by The International Union of Biochemistry and Molecular Biology.