Robinson Andrew J, Love Christopher G, Batley Jacqueline, Barker Gary, Edwards David
Plant Biotechnology Centre, Primary Industries Research Victoria, La Trobe University, Bundoora 3086, Victoria, Australia.
Bioinformatics. 2004 Jun 12;20(9):1475-6. doi: 10.1093/bioinformatics/bth104. Epub 2004 Feb 12.
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.
This program has been written in PERL and is freely available for non-commercial users by request from the authors. The Web-based version may be accessed at http://hornbill.cspp.latrobe.edu.au/
简单序列重复（SSRs）已成为广泛应用的重要分子标记，如基因组图谱绘制与特征分析、表型图谱绘制、作物的标记辅助选择以及一系列分子生态学和多样性研究。随着DNA序列信息可用性的增加，用于识别和设计用于扩增SSR位点的PCR引物的自动化程序将成为植物育种计划中的有用工具。我们报告了一种应用程序，它将SSR重复序列查找工具SPUTNIK与PCR引物设计程序Primer3整合到一个管道工具SSR Primer中。提交多个FASTA格式的序列后，该脚本使用SPUTNIK在每个序列中筛选SSR。结果被解析到Primer3进行位点特异性引物设计。该脚本使用基于Web的界面，支持远程使用。
该程序用PERL编写，非商业用户可向作者申请免费获取。基于Web的版本可在http://hornbill.cspp.latrobe.edu.au/访问。
