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首页> 外文会议>IEEE International Conference on Bioinformatics and Biomedicine >SNPViz v2.0: A web-based tool for enhanced haplotype analysis using large scale resequencing datasets and discovery of phenotypes causative gene using allelic variations
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SNPViz v2.0: A web-based tool for enhanced haplotype analysis using large scale resequencing datasets and discovery of phenotypes causative gene using allelic variations

机译：SNPVIZ v2.0：使用大规模重置数据集和使用等位基因变异的表型引起的成因基因的增强单倍型分析的基于Web的单倍型分析

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Single nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) are widely spread across all chromosomes of the genome and act as biological markers, which aid in identification of genes associated with traits or phenotypes. With the advances in next-generation sequencing (NGS) technology, large amounts of SNPs and Indels data have become available, making it difficult to effectively perform analysis across multiple samples and intuitively integrate, compare and/or visualize them simultaneously. Genome-wide association studies (GWAS) is a widely used method to find genetic variations associated with a trait, but it lacks an efficient way to investigate genomic variant functions. To tackle these issues, we have developed SNPViz v2.0, a web-based tool to visualize large-scale haplotype blocks with detailed SNPs and Indels grouped by their chromosomal coordinates, along with their overlapping gene models, phenotype to genotype accuracies, Gene Ontology (GO) annotations, protein families (Pfam) annotations, genomic variant annotations, and their functional effects. Moreover, SNPViz v2.0 integrates several large scale soybean SNPs and Indels datasets including G. Soja, GWAS, NAM41, USB-15x, USB-40x, MSMC and Zhou302, available from multiple studies. SNPViz v2.0 is deployed for all organisms and available in both SoyKB and KBCommons frameworks. For soybean data only, the SNPViz 2.0 is publicly available at http://soykb.org/SNPViz2/. For other organisms such as Arabidopsis thaliana, Mus musculus and Zea mays, SNPViz 2.0 is publicly available in their respective knowledge bases at https://kbcommons.org.
机译：单核苷酸多态性（SNP）和插入/缺失（吲哚）在基因组的所有染色体上广泛蔓延，并充当生物标志物，这有助于鉴定与特征或表型相关的基因。随着下一代测序（NGS）技术的进展，大量的SNP和indels数据可用，使得难以在多个样本上有效地进行分析，并直观地集成，比较和/或同时可视化它们。基因组 - 范围的协会研究（GWAS）是一种广泛使用的方法，用于找到与特征相关的遗传变异，但它缺乏调查基因组变异功能的有效方法。为了解决这些问题，我们开发了SNPVIZ v2.0，是一种基于Web的工具，可视化具有由其染色体坐标的详细的SNP和诱导的大规模单倍型块，以及它们的重叠基因模型，基因型精度，基因本体的表型（GO）注释，蛋白质家族（PFAM）注释，基因组变异注释及其功能效果。此外，SNPVIZ V2.0集成了几种大型大豆SNP和Indels数据集，包括G. Soja，Gwas，Nam41，USB-15x，USB-40X，MSMC和Zhou302，可从多项研究中获得。 SNPVIZ V2.0部署所有有机体，并在Soykb和Kbcommons框架中提供。仅用于大豆数据，SNPVIZ 2.0在http://soykb.org/snpviz2/上公开提供。对于其他生物，如拟南芥，Mus Musculus和Zea Mays，SNPVIZ 2.0在HTTPS://kbcommons.org上公开提供各自的知识库。

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