Teaching genomics and bioinformatics to undergraduates using java

In this paper, we describe Java software that can be used to expose undergraduates to genomics. The content and software developed provide multidisciplinary knowledge to undergraduates in signal processing, genetics and statistics. DNA, which is the fundamental storehouse of genetic information, is a linear polymer formed from four sub-units called nucleotides. The Java software is embedded in the ASU J-DSP visual programming environment. We have developed Java-DSP modules to present basic concepts about nucleotide character sequences. Specific J-DSP functions to analyze DNA sequences include: Numerical Mapping, FFT Power Spectrum, and Amino Acid Sequencing. Using the Numerical Mapping function, nucleotide sequences can be transformed into the numerical domain through binary, complex or integer number mappings. The FFT Power Spectrum block is used to compute the power spectrum of mapped sequences, and further classify them as belonging to either protein coding or non-coding regions. The above J-DSP blocks can also be integrated to form an internet visualization tool to identify genes in unannotated DNA sequences. A typical scenario is for a student to read a high-level DNA tutorial and execute our Java simulations. A series of learning modules and accompanying web-based exercises have also been developed. Exercises include: DNA fundamentals, numerical mapping of nucleotides, DNA power spectrum computation, and amino acid sequencing. The software and hands-on exercises have been assigned and assessed in the undergraduate DSP class at ASU.