A comparative analysis of existing oligonucleotides selection algorithms for microarray technology

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 cuniculi and human genomes. The analysis also shows that a large number of the existing tools are difficult to install and configure. For cross hybridization test, most rely on BLAST and therefore design ill specific oligonucleotides. Furthermore, most are non-intuitive to use and lack important oligo design and software features