In silico PCR-RFLP of Bacillus Species: Problem-Based Case of Teaching Bioinformatics

Abstract

Bioinformatics is a multi-disciplinary subject that encompasses a wide range of fields including; genomics, biotechnology, information technology, algorithms and statistics. As a result, it is important to establish a skeletal set of courses capable of providing both a general and a detailed background on all aspects of bioinformatics. In this study, a problem-based project entitled “in silico PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism) of Bacillus species” was assigned to students. The project aimed to cover the background of genetic information retrieval, multiple sequence alignment, phylogenetic analysis and in silico PCR-RFLP. Initially, the 16S rRNA genes of 34 Bacillus species were retrieved from the NCBI database. The sequence data obtained were then analyzed in terms of their similarities and variation using the ClustalW software. Subsequently, the phylogenetic tree was constructed to investigate their evolutionary relationship. The results indicated that these Bacillus species could be grouped into different clades. In addition, in silico PCR-RFLP was performed to introduce students to the principles of molecular taxonomy.