Simple sequence repeat marker loci discovery using SSR primer
Simple sequence repeat marker loci discovery using SSR primer
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DOI：
10.1093/bioinformatics/bth104
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发表时间：
2004-06-12
期刊：
影响因子：
5.8
通讯作者：
Edwards, D
中科院分区：
文献类型：
--
作者：
Robinson, AJ;Love, CG;Edwards, D
简单重复序列（SSR）已成为重要的分子标记，在基因组作图、表型作图、作物标记辅助选择以及分子生态学和多样性研究等方面有着广泛的应用。随着DNA序列信息的增加，自动化的方法来识别和设计PCR引物扩增SSR位点将是一个有用的工具，在植物育种计划。我们报告了一个应用程序，集成SPUTNIK，SSR重复发现，引物3，PCR引物设计程序，到一个管道工具，SSR引物。在提交多个FASTA格式的序列时，脚本使用SPUTNIK筛选每个序列的SSR。将结果解析为Primer3用于基因座特异性引物设计。该脚本使用基于Web的界面，支持远程使用。
Simple sequence repeats (SSRs) have become important molecular markers for a broad range of applications, such as genome mapping and characterization, phenotype mapping, marker assisted selection of crop plants and a range of molecular ecology and diversity studies. With the increase in the availability of DNA sequence information, an automated process to identify and design PCR primers for amplification of SSR loci would be a useful tool in plant breeding programs. We report an application that integrates SPUTNIK, an SSR repeat finder, with Primer3, a PCR primer design program, into one pipeline tool, SSR Primer. On submission of multiple FASTA formatted sequences, the script screens each sequence for SSRs using SPUTNIK. The results are parsed to Primer3 for locus-specific primer design. The script makes use of a Web-based interface, enabling remote use.