Premkrishnan Balakrishnan Vasanthakumari, Arunachalam Vadivel
Department of Computational Biology & Bioinformatics, North Campus-Kariavattom, University of Kerala, Thiruvananthapuram, Kerala 695581, India.
Comp Funct Genomics. 2012;2012:913709. doi: 10.1155/2012/913709. Epub 2012 Mar 13.
RAPD is a simple dominant marker system widely used in biology. Effectiveness of RAPD can be improved by selecting and redesigning primers whose priming sites occur in target sequence(s) of gene or organism at optimum distance. We developed software that uses sequences of random decamer primers and nucleotide sequence(s) as two input files. It locates the priming sites in input sequences and generates output files listing frequency and distance between priming sites. When the priming sites of a single primer occur more than once in a sequence with a distance of 200 to 2000 bp, the software also designs pairs of iSCAR primers. An input of 387 RAPD primers and 42,432 expressed sequences of oil palm are used as test. Wet-lab PCR results from a publication that used the same set of primers were compared with software output on priming sites. In the test sequences of oil palm covering 1.4% of genome, we found that at least 60% the primers chosen using software are sure of giving PCR amplification. We designed 641 iSCAR primers suitable for amplification of oil palm DNA. The software successfully predicted 92% (67 out of 73) of published polymorphic RAPD primers in oil palm.
随机扩增多态性DNA（RAPD）是一种广泛应用于生物学的简单显性标记系统。通过选择和重新设计引物，使其引发位点在基因或生物体的靶序列中以最佳距离出现，可以提高RAPD的有效性。我们开发了一种软件，该软件将随机十聚体引物序列和核苷酸序列作为两个输入文件。它在输入序列中定位引发位点，并生成列出引发位点之间频率和距离的输出文件。当单个引物的引发位点在序列中出现不止一次且距离为200至2000 bp时，该软件还会设计成对的内部简单序列重复区间（iSCAR）引物。使用387个RAPD引物和42432个油棕表达序列作为测试输入。将一篇使用相同引物集的出版物中的湿实验室聚合酶链反应（PCR）结果与软件在引发位点上的输出进行比较。在覆盖油棕基因组1.4%的测试序列中，我们发现使用该软件选择的引物中至少60%肯定能进行PCR扩增。我们设计了641个适合扩增油棕DNA的iSCAR引物。该软件成功预测了油棕中已发表的多态性RAPD引物的92%（73个中的67个）。
