• 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>Genes and genomics >RISA: a new web-tool for Rapid Identification of SSRs and Analysis of primers
【24h】

RISA: a new web-tool for Rapid Identification of SSRs and Analysis of primers

机译：RISA：一种用于快速鉴定SSR和分析引物的新网络工具

获取原文
获取原文并翻译 | 示例
           
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

The simple sequence repeats (SSRs) are short tandem arrayed sequence motifs consisting of 2-6 bp, which are not only involved in causing human fatal diseases but also have various applications in plant genetic studies. Thanks to the advancements madein sequencing technology, now we can easily generate genomic/transcriptomic sequences in a shorter period of time. Therefore, trend to identify SSR markers needs up gradation to handle these high-throughput data. Unfortunately, existing web programs foridentifying SSR markers are useful but they are unable to process high-throughput data. To overcome this disadvantage, we have constructed a web-based tool, RISA (http://sol.kribb.re.kr/RISA/), with a goal of one-click service to identify SSR markers from high-throughput data (up to 200 Mbp). RISA controls automatic input and output pipeline by demon which combines the SSR classification and investigation by Robert Kofler (SciRoKo) to search SSRs and Primer3 to identify primers specific to SSRs simultaneously. In our test, 45,495 qualified primer sets specific to 47,070 SSRs were identified by RISA from whole Arabidopsis lyrata genome (about 207 Mbp) in 15 minutes. In results, it includes SSR statistics generated from user's queries and SSR markers information along with primers suitable for their amplification. To support handling of large amount of results, RISA provides various filtering options such as motif length, repeat units, total length and PCR product size. Therefore, we propose that RISA minimizes labour-intensive works or any other considerations which can be required during the development of SSR markers withouthaving deep understanding of computer system and/or algorithms.
机译：简单序列重复序列（SSR）是由2-6 bp组成的短串联排列的序列基序，不仅涉及导致人类致命疾病的原因，而且在植物遗传研究中具有多种应用。得益于测序技术的进步，现在我们可以在更短的时间内轻松生成基因组/转录组序列。因此，识别SSR标记的趋势需要逐步升级才能处理这些高通量数据。不幸的是，用于识别SSR标记的现有Web程序很有用，但它们无法处理高通量数据。为克服此缺点，我们构建了一个基于Web的工具RISA（http://sol.kribb.re.kr/RISA/），其目的是提供一键式服务以从高通量数据中识别SSR标记（最高200 Mbp）。 RISA通过恶魔控制自动输入和输出管线，该程序结合了SSR分类和Robert Kofler（SciRoKo）的研究，以搜索SSR和Primer3，以同时识别特定于SSR的引物。在我们的测试中，RISA在15分钟内从整个拟南芥全基因组基因组（约207 Mbp）中鉴定了针对47,070个SSR的45,495个合格引物。结果，它包括从用户查询生成的SSR统计信息和SSR标记信息以及适合其扩增的引物。为了支持处理大量结果，RISA提供了各种过滤选项，例如基序长度，重复单元，总长度和PCR产物大小。因此，我们建议RISA尽量减少劳动密集型工作或在开发SSR标记时可能需要的任何其他考虑因素，而无需对计算机系统和/或算法有深入的了解。

著录项

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号