Jewell Erica, Robinson Andrew, Savage David, Erwin Tim, Love Christopher G, Lim Geraldine A C, Li Xi, Batley Jacqueline, Spangenberg German C, Edwards David
Department of Primary Industries, Plant Biotechnology Centre, Primary Industries Research Victoria, Victorian AgriBiosciences Centre, 1 Park Drive, Bundoora, Victoria 3083, Australia.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W656-9. doi: 10.1093/nar/gkl083.
Simple sequence repeat (SSR) molecular genetic markers have become important tools for a broad range of applications such as genome mapping and genetic diversity studies. SSRs are readily identified within DNA sequence data and PCR primers can be designed for their amplification. These PCR primers frequently cross amplify within related species. We report a web-based tool, SSR Primer, that integrates SPUTNIK, an SSR repeat finder, with Primer3, a primer design program, within one pipeline. On submission of multiple FASTA formatted sequences, the script screens each sequence for SSRs using SPUTNIK. Results are then parsed to Primer3 for locus specific primer design. We have applied this tool for the discovery of SSRs within the complete GenBank database, and have designed PCR amplification primers for over 13 million SSRs. The SSR Taxonomy Tree server provides web-based searching and browsing of species and taxa for the visualisation and download of these SSR amplification primers. These tools are available at http://bioinformatics.pbcbasc.latrobe.edu.au/ssrdiscovery.html.
简单序列重复（SSR）分子遗传标记已成为广泛应用的重要工具，如基因组图谱绘制和遗传多样性研究。SSR很容易在DNA序列数据中识别出来，并且可以设计PCR引物对其进行扩增。这些PCR引物经常在相关物种中交叉扩增。我们报告了一个基于网络的工具SSR Primer，它在一个流程中整合了SSR重复序列查找工具SPUTNIK和引物设计程序Primer3。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。然后将结果解析到Primer3进行位点特异性引物设计。我们已将此工具应用于在完整的GenBank数据库中发现SSR，并为超过1300万个SSR设计了PCR扩增引物。SSR分类树服务器提供基于网络的物种和分类单元搜索与浏览，以可视化和下载这些SSR扩增引物。这些工具可在http://bioinformatics.pbcbasc.latrobe.edu.au/ssrdiscovery.html获取。
