A DNA Probe Design System Based On K-mer Similarity Algorithm

With the growth of genome data, the development of oligonucleotide synthesis and DN A microarray technology, oligonucleotide arrays have become one of the most widely used molecular tools. Their detection accuracy largely depends on the quality of DN A probes. Therefore, it is very important to design DN A probes with high specificity, sensitivity and uniformity. The efficiency of DN A probe design should also be considered with the huge sequence data in current.In this paper, a global alignment algorithm, K- mer Similarity, which takes the advantage of the characteristics of sequence alignment proble m in probe design is proposed. It obtains the same results as N eedleman- Wunsch algorithm, while executing 60 times faster. A probe design system based on K- mer Similarity algorithm is designed and imple mented, which provides a fast and high quality DNA probe design service.Most factors that influence the specificity, sensitivity and uniformity of DN A probes are considered in the system, such as the low complexity regions, maximum contiguous stretches, maximum similarity between the probes and non- target sequences, GC content, melt ing temperature, and freedom energy. This guarantees the quality of DNA probes designed. In addition, the system can not only design specific probes, but also group probes for those with no specific probes.At the end of this paper, the system is tested. First, we tested the main modules of the system. The results show that the system works well and meets the purpose. Second, the core algorithm, K- mer Similarity, is tested. The comparison between K-mer Similarity and other algorithms s hows that K- mer Similarity has a high efficiency while ensuring the accuracy. We tested the efficiency of the whole system at last. Compared with preexisting DN A probe design software tools, the system performs well and it is a good choice for DNA probe design.