Heuristic Probe Mining Based on Multiple Sequence Analysis

Figure 1: The procedures of the proposed method. In the technology of DNA chips and cDNA microarrays, there is a great deal of studies on composing oligo DNA on the DNA chip and the cDNA microarray by the present situation, but there are a few studies on designing oligo DNA sequences, which are fixed on the DNA chip and the cDNA microarray [4]. Probe design is the essential procedure for high-throughput research such as the oligonucleotide chip, sequencing by hybridization, and etc. The PCR technology, including RT-PCR and Multiplex PCR, is one of the most important techniques in molecular biology. Therefore it is also highly desired to develop a method of PCR primer design for successful experiments. There are a lot of studies for PCR primer design [5]. And Kurata and Nakmura presented primer/probe design method suitable to whole genome experiment [3]. However, it is difficult to apply the existing method to design both genusand speciesspecific probe at a time. This paper shows the heuristic method to extract two kind of probes from the MSA(multiple sequence analysis) result of target sequences. The first kind of probes is for detecting conserved regions and the other is for sequence specific regions. The results are compared with probes of commercial oligo DNA chip which can identify 21 Mycobacteria species.