Simple sequence repeats (SSRs) are regions in DNA sequence that contain repeating motifs of length 1–6 nucleotides. These repeats are ubiquitously present and are found in both coding and non-coding regions of genome. A total of 534 complete chloroplast genome sequences (as on 18 September 2014) of Viridiplantae are available at NCBI organelle genome resource. It provides opportunity to mine these genomes for the detection of SSRs and store them in the form of a database. In an attempt to properly manage and retrieve chloroplastic SSRs, we designed ChloroSSRdb which is a relational database developed using SQL server 2008 and accessed through ASP.NET. It provides information of all the three types (perfect, imperfect and compound) of SSRs. At present, ChloroSSRdb contains 124 430 mined SSRs, with majority lying in non-coding region. Out of these, PCR primers were designed for 118 249 SSRs. Tetranucleotide repeats (47 079) were found to be the most frequent repeat type, whereas hexanucleotide repeats (6414) being the least abundant. Additionally, in each species statistical analyses were performed to calculate relative frequency, correlation coefficient and chi-square statistics of perfect and imperfect SSRs. In accordance with the growing interest in SSR studies, ChloroSSRdb will prove to be a useful resource in developing genetic markers, phylogenetic analysis, genetic mapping, etc. Moreover, it will serve as a ready reference for mined SSRs in available chloroplast genomes of green plants.>Database URL:
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机译:简单序列重复(SSR)是DNA序列中包含长度为1-6个核苷酸的重复基序的区域。这些重复序列普遍存在,并在基因组的编码区和非编码区中都发现。在NCBI细胞器基因组资源中可获得共534个Viridiplantae的叶绿体基因组完整序列(截至2014年9月18日)。它提供了挖掘这些基因组以检测SSR并将其以数据库形式存储的机会。为了适当地管理和检索叶绿体SSR,我们设计了ChloroSSRdb,它是使用SQL Server 2008开发并通过ASP.NET访问的关系数据库。它提供了所有三种类型的SSR(完美,不完美和复合)的信息。目前,ChloroSSRdb包含124至430个已开采的SSR,大部分位于非编码区域。其中,PCR引物设计用于118 249个SSR。发现四核苷酸重复序列(47→079)是最常见的重复类型,而六核苷酸重复序列(6414)的序列最少。此外,对每个物种进行统计分析,以计算出完善和不完善的SSR的相对频率,相关系数和卡方统计。随着对SSR研究的兴趣不断增长,ChloroSSRdb将被证明是开发遗传标记,系统发育分析,遗传作图等方面的有用资源。此外,它将为绿色植物可用叶绿体基因组中的已开采SSR提供参考。 。>数据库URL: strong>
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