Chuang Li-Yeh, Yang Cheng-Hong, Cheng Yu-Huei, Gu De-Leung, Chang Phei-Lang, Tsui Ke-Hung, Chang Hsueh-Wei
Department of Chemical Engineering, I-Shou University, 840, Taiwan.
BMC Bioinformatics. 2006 Aug 15;7:379. doi: 10.1186/1471-2105-7-379.
Mitochondrial single nucleotide polymorphisms (mtSNPs) constitute important data when trying to shed some light on human diseases and cancers. Unfortunately, providing relevant mtSNP genotyping information in mtDNA databases in a neatly organized and transparent visual manner still remains a challenge. Amongst the many methods reported for SNP genotyping, determining the restriction fragment length polymorphisms (RFLPs) is still one of the most convenient and cost-saving methods. In this study, we prepared the visualization of the mtDNA genome in a way, which integrates the RFLP genotyping information with mitochondria related cancers and diseases in a user-friendly, intuitive and interactive manner. The inherent problem associated with mtDNA sequences in BLAST of the NCBI database was also solved.
V-MitoSNP provides complete mtSNP information for four different kinds of inputs: (1) color-coded visual input by selecting genes of interest on the genome graph, (2) keyword search by locus, disease and mtSNP rs# ID, (3) visualized input of nucleotide range by clicking the selected region of the mtDNA sequence, and (4) sequences mtBLAST. The V-MitoSNP output provides 500 bp (base pairs) flanking sequences for each SNP coupled with the RFLP enzyme and the corresponding natural or mismatched primer sets. The output format enables users to see the SNP genotype pattern of the RFLP by virtual electrophoresis of each mtSNP. The rate of successful design of enzymes and primers for RFLPs in all mtSNPs was 99.1%. The RFLP information was validated by actual agarose electrophoresis and showed successful results for all mtSNPs tested. The mtBLAST function in V-MitoSNP provides the gene information within the input sequence rather than providing the complete mitochondrial chromosome as in the NCBI BLAST database. All mtSNPs with rs number entries in NCBI are integrated in the corresponding SNP in V-MitoSNP.
V-MitoSNP is a web-based software platform that provides a user-friendly and interactive interface for mtSNP information, especially with regard to RFLP genotyping. Visual input and output coupled with integrated mtSNP information from MITOMAP and NCBI make V-MitoSNP an ideal and complete visualization interface for human mtSNPs association studies.
线粒体单核苷酸多态性（mtSNPs）在试图阐明人类疾病和癌症时构成重要数据。不幸的是，以一种组织有序且透明的可视化方式在mtDNA数据库中提供相关的mtSNP基因分型信息仍然是一项挑战。在报道的众多SNP基因分型方法中，确定限制性片段长度多态性（RFLPs）仍然是最便捷且最节省成本的方法之一。在本研究中，我们以一种将RFLP基因分型信息与线粒体相关癌症和疾病以用户友好、直观且交互式的方式整合的方法，对mtDNA基因组进行了可视化处理。同时也解决了NCBI数据库中BLAST里与mtDNA序列相关的固有问题。
V-MitoSNP为四种不同类型的输入提供完整的mtSNP信息：（1）通过在基因组图谱上选择感兴趣的基因进行颜色编码的可视化输入；（2）按基因座、疾病和mtSNP rs# ID进行关键词搜索；（3）通过点击mtDNA序列的选定区域进行核苷酸范围的可视化输入；（4）序列mtBLAST。V-MitoSNP输出为每个SNP提供500个碱基对（bp）的侧翼序列，以及RFLP酶和相应的天然或错配引物组。输出格式使用户能够通过对每个mtSNP进行虚拟电泳来查看RFLP的SNP基因型模式。所有mtSNP中RFLP酶和引物的成功设计率为99.1%。RFLP信息通过实际琼脂糖电泳进行了验证，并且所有测试的mtSNP均显示出成功的结果。V-MitoSNP中的mtBLAST功能提供输入序列内的基因信息，而不像NCBI BLAST数据库那样提供完整的线粒体染色体。NCBI中所有有rs编号条目的mtSNP都整合到了V-MitoSNP的相应SNP中。
V-MitoSNP是一个基于网络的软件平台，为mtSNP信息提供了用户友好且交互式的界面，特别是在RFLP基因分型方面。可视化的输入和输出，再加上来自MITOMAP和NCBI的整合mtSNP信息，使V-MitoSNP成为人类mtSNP关联研究的理想且完整的可视化界面。
