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BiSearch网络服务器。

The BiSearch web server.

作者信息

Arányi Tamás, Váradi András, Simon István, Tusnády Gábor E

机构信息

lnstitute of Enzymology, BRC, HAS, H-1113 Karolina út 29, Budapest, Hungary.

出版信息

BMC Bioinformatics. 2006 Oct 5;7:431. doi: 10.1186/1471-2105-7-431.

DOI:10.1186/1471-2105-7-431
PMID:17022803
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC1609187/
Abstract

BACKGROUND

A large number of PCR primer-design softwares are available online. However, only very few of them can be used for the design of primers to amplify bisulfite-treated DNA templates, necessary to determine genomic DNA methylation profiles. Indeed, the number of studies on bisulfite-treated templates exponentially increases as determining DNA methylation becomes more important in the diagnosis of cancers. Bisulfite-treated DNA is difficult to amplify since undesired PCR products are often amplified due to the increased sequence redundancy after the chemical conversion. In order to increase the efficiency of PCR primer-design, we have developed BiSearch web server, an online primer-design tool for both bisulfite-treated and native DNA templates.

RESULTS

The web tool is composed of a primer-design and an electronic PCR (ePCR) algorithm. The completely reformulated ePCR module detects potential mispriming sites as well as undesired PCR products on both cDNA and native or bisulfite-treated genomic DNA libraries. Due to the new algorithm of the current version, the ePCR module became approximately hundred times faster than the previous one and gave the best performance when compared to other web based tools. This high-speed ePCR analysis made possible the development of the new option of high-throughput primer screening. BiSearch web server can be used for academic researchers at the http://bisearch.enzim.hu site.

CONCLUSION

BiSearch web server is a useful tool for primer-design for any DNA template and especially for bisulfite-treated genomes. The ePCR tool for fast detection of mispriming sites and alternative PCR products in cDNA libraries and native or bisulfite-treated genomes are the unique features of the new version of BiSearch software.

摘要

背景

网上有大量的PCR引物设计软件。然而，其中只有极少数可用于设计扩增亚硫酸氢盐处理的DNA模板的引物，而这对于确定基因组DNA甲基化谱是必需的。实际上，随着DNA甲基化检测在癌症诊断中变得愈发重要，针对亚硫酸氢盐处理模板的研究数量呈指数级增长。亚硫酸氢盐处理的DNA难以扩增，因为化学转化后序列冗余增加，常常会扩增出不需要的PCR产物。为提高PCR引物设计的效率，我们开发了BiSearch网络服务器，这是一种用于亚硫酸氢盐处理和天然DNA模板的在线引物设计工具。

结果

该网络工具由引物设计和电子PCR（ePCR）算法组成。经过全面重新设计的ePCR模块可检测cDNA以及天然或亚硫酸氢盐处理的基因组DNA文库中的潜在错配位点和不需要的PCR产物。由于当前版本采用了新算法，ePCR模块的速度比上一版本快了约100倍，与其他基于网络的工具相比性能最佳。这种高速的ePCR分析使得高通量引物筛选的新选项得以开发。BiSearch网络服务器可供学术研究人员在http://bisearch.enzim.hu网站使用。

结论

BiSearch网络服务器是用于任何DNA模板，尤其是亚硫酸氢盐处理基因组的引物设计的有用工具。用于快速检测cDNA文库以及天然或亚硫酸氢盐处理基因组中的错配位点和替代PCR产物的ePCR工具是新版BiSearch软件的独特功能。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f9/1609187/6672c6c9c516/1471-2105-7-431-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f9/1609187/ede1f4a7d353/1471-2105-7-431-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f9/1609187/6672c6c9c516/1471-2105-7-431-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f9/1609187/ede1f4a7d353/1471-2105-7-431-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71f9/1609187/6672c6c9c516/1471-2105-7-431-2.jpg

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