BLASTmap: A Shiny-Based Application to Visualize BLAST Results as Interactive Heat Maps and a Tool to Design Gene-Specific Baits for Bespoke Target Enrichment Sequencing.
BLASTmap: A Shiny-Based Application to Visualize BLAST Results as Interactive Heat Maps and a Tool to Design Gene-Specific Baits for Bespoke Target Enrichment Sequencing.
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DOI：
10.1007/978-1-4939-8724-5_14
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发表时间：
2018
影响因子：
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通讯作者：
Katie Baker;Gordon Stephen;Shona M Strachan;M. Armstrong;I. Hein
中科院分区：
文献类型：
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作者：
Katie Baker;Gordon Stephen;Shona M Strachan;M. Armstrong;I. Hein
目前正在发现许多决定植物-病原体相互作用结果的基因，包括例如免疫受体、易感因子和病原体效应子及其宿主靶标。靶富集测序提供了优先对这些感兴趣的基因进行重测序而不需要首先产生基因型特异性基因组组装的手段。基本局部比对搜索工具（BLAST）与本文开发的BLAST图谱组合，可用于设计特异性靶向此类基因的探针，通过使用靶物种或最接近的相关属作为参考。BLAST是生物序列分析中普遍存在的工具，并且许多程序可用于可视化BLAST比对。然而，目前还没有专门的程序用于视觉比较大规模BLAST输出属性，如位得分。需要快速和有效地比较成千上万的BLAST结果导致了BLASTmap的开发，这是一个使用Shiny R包创建的交互式Web应用程序，定制用于聚类和查看BLAST结果作为交互式热图。在这里，我们展示了一个BLASTmap如何成功地应用于分析定制的DNA/RNA探针序列，并直观地确定四个探针是足够的特异性，但包括丰富的马铃薯R2抗病基因家族的例子。
Numerous genes that determine the outcome of plant–pathogen interactions are currently being discovered and include, for example, immune receptors, susceptibility factors and pathogen effectors and their host targets. Target enrichment sequencing provides a means to preferentially resequence these genes of interest without the need to first generate a genotype-specific genome assembly. The Basic Local Alignment Search Tool (BLAST), in combination with the here developed BLASTmap, can be used to design probes that specifically target such gene(s), either by using the target species or the closest related genus as a reference. BLAST is a ubiquitous tool in biological sequence analysis and a multitude of programs are available for the visualization of BLAST alignments. However, there are currently no dedicated programs for visual comparison of large-scale BLAST output attributes such as bit score. The need to quickly and efficiently compare many thousands of BLAST results led to the development of BLASTmap, an interactive web application created using the Shiny R package, customized for clustering and viewing BLAST results as an interactive heat map. Here we show an example of how BLASTmap was successfully applied to analyze custom DNA/RNA probe sequences and to visually determine that four probes are sufficient for the specific yet inclusive enrichment of the potatoR2disease resistance gene family.