Yesprit and Yeaseq: Applications for designing primers and browsing sequences for research using the four Schizosaccharomyces species,Yeast

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Yesprit and Yeaseq: Applications for designing primers and browsing sequences for research using the four Schizosaccharomyces species
Yeast ( IF 2.2 ) Pub Date : 2021-07-12 , DOI: 10.1002/yea.3660
Xindi Wang ₁ , Ruoming Xu ₁ , Yichen Wang ₁ , Ziyue Liu ₁ , Ronghui Lou _{1,

2} , Tomoyasu Sugiyama ₁

Affiliation

The polymerase chain reaction (PCR)-based gene targeting method, which can delete a specific gene or introduce tags, has been widely utilized to study gene function in fission yeast. One of the critical steps in this method is to design primers for amplifying DNA fragments of deletion or tagging modules and for checking the integration of those DNA fragments at designated loci. Although the primer design tool Pombe PCR Primer Program (PPPP) is available for Schizosaccharomyces pombe, there is no such publicly available application for the other three fission yeast species, S. cryophilus, S. japonicus, and S. octosporus. Likewise, no application enabling DNA/protein sequence retrieval for these three fission yeast species is available either. Therefore, access to such functionality would substantially assist in retrieval of gene sequences of interest and primer design in these fission yeast species. In this report, we describe two applications for fission yeast study: Yesprit and Yeaseq. Yesprit is a primer design tool for strain construction using the PCR-based method, and Yeaseq is a sequence viewer that can acquire the DNA/protein sequences of specific genes. Both tools can be run on the Windows, macOS, and Linux platforms. We believe that the Yesprit and Yeaseq will facilitate research using the four fission yeast species.

中文翻译：

Yesprit 和 Yeaseq：用于设计引物和浏览序列以使用四种裂殖酵母菌进行研究的应用

基于聚合酶链式反应 (PCR) 的基因靶向方法可以删除特定基因或引入标签，已被广泛用于研究裂殖酵母中的基因功能。该方法的关键步骤之一是设计引物，用于扩增缺失或标记模块的 DNA 片段，并检查这些 DNA 片段在指定位点的整合。虽然引物设计工具 Pombe PCR Primer Program (PPPP) 可用于粟酒裂殖酵母，但对于其他三种裂殖酵母菌，即嗜冷链霉菌、日本猪链霉菌和章孢链霉菌，却没有此类公开可用的应用程序。. 同样，也没有应用程序能够对这三种裂殖酵母物种进行 DNA/蛋白质序列检索。因此，获得这种功能将大大有助于检索这些裂殖酵母物种中感兴趣的基因序列和引物设计。在本报告中，我们描述了裂变酵母研究的两种应用：Yesprit 和 Yeaseq。Yesprit 是使用基于 PCR 的方法构建菌株的引物设计工具，而 Yeaseq 是可以获取特定基因的 DNA/蛋白质序列的序列查看器。这两种工具都可以在 Windows、macOS 和 Linux 平台上运行。我们相信 Yesprit 和 Yeaseq 将促进使用四种裂殖酵母物种的研究。

更新日期：2021-07-12

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