Full Length Research Paper
Abstract
In system biology, DNA microarray technology is an indispensable tool for the biological analysis involved at the level of the whole genome. Among the sophisticated analytical problems in microarray technology at the front and back ends, respectively, are the selection of optimal DNA oligonucleotides (henceforth oligos) and computational analysis of the genes expression data. A computational comparative analysis of the methods used to select oligos is important since the design and quality of the microarray probes are of critical importance for the hybridization experiments as well as subsequent analysis of the data. In an attempt to enhance efficient and effective design at the front end, a computational comparative analysis was performed on oligos selection tools using the barley ESTs, as well as the Saccharomyces cerevisiae, Encephalitozoon cuniculiand human genomes. The analysis also shows that a large number of the existing tools are difficult to install and conï¬gure. For cross hybridization test, most rely on BLAST and therefore design ill speciï¬c oligonucleotides. Furthermore, most are non-intuitive to use and lack important oligo design and software features.
Key words: System biology, microarray technology, oligo, genome, coding sequence, expressed sequence tag (EST).
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