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首页> 外文期刊>Comparative and functional genomics >In Silico RAPD Priming Sites in Expressed Sequences and iSCAR Markers for Oil Palm
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In Silico RAPD Priming Sites in Expressed Sequences and iSCAR Markers for Oil Palm

机译：表达序列中的Silico RAPD启动位点和油棕的iSCAR标记

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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.
机译：RAPD是广泛用于生物学的简单显性标记系统。通过选择和重新设计其引物位点位于基因或生物体的目标序列中最佳距离的引物，可以提高RAPD的有效性。我们开发了使用随机decamer引物序列和核苷酸序列作为两个输入文件的软件。它按输入顺序定位启动部位，并生成列出启动部位之间的频率和距离的输出文件。当单个引物的引物位点在200到2000bp的序列中出现多次时，该软件还会设计成对的iSCAR引物。使用387个RAPD引物和42,432个表达的油棕序列输入作为测试。将使用同一套引物的出版物的湿实验室PCR结果与引物位点上的软件输出进行比较。在覆盖1.4％基因组的油棕测试序列中，我们发现使用软件选择的引物中至少有60％确实可以进行PCR扩增。我们设计了641个iSCAR引物，适合扩增油棕DNA。该软件成功预测了油棕中92％（73个中的67个）已发布的多态RAPD引物。

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