A design method of DNA chips for SNP analysis using self-organizing maps

We introduce a design method of DNA chips using self-organizing maps (SOM). DNA chips are powerful tools for sequencing and SNP (single nucleotide polymorphism) analyses of DNA sequences. A DNA chip is an array of DNA probes which are hybridized with the compliment sub-sequences in the target sequence. However, conventional DNA chips are showing tendency to be comprised of longer probes and get larger in size to achieve a higher resolution. To shrink the size of DNA chips, the design is considered to be important. To solve this problem, we applied SOM to obtain common features of DNA sequences with small number of probes which efficiently cover the target sequence with sufficient resolution for finding the correct position of SNPs. We evaluated the DNA chips designed by SOM with computer simulations of SNP analyses, changing the length of probes and size of the maps