MU Institute for Data Science and Informatics, University of Missouri-Columbia, Columbia, MO, USA.
Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, USA.
BMC Genomics. 2023 Mar 10;24(1):107. doi: 10.1186/s12864-023-09161-3.
The advancement of sequencing technologies today has made a plethora of whole-genome re-sequenced (WGRS) data publicly available. However, research utilizing the WGRS data without further configuration is nearly impossible. To solve this problem, our research group has developed an interactive Allele Catalog Tool to enable researchers to explore the coding region allelic variation present in over 1,000 re-sequenced accessions each for soybean, Arabidopsis, and maize.
The Allele Catalog Tool was designed originally with soybean genomic data and resources. The Allele Catalog datasets were generated using our variant calling pipeline (SnakyVC) and the Allele Catalog pipeline (AlleleCatalog). The variant calling pipeline is developed to parallelly process raw sequencing reads to generate the Variant Call Format (VCF) files, and the Allele Catalog pipeline takes VCF files to perform imputations, functional effect predictions, and assemble alleles for each gene to generate curated Allele Catalog datasets. Both pipelines were utilized to generate the data panels (VCF files and Allele Catalog files) in which the accessions of the WGRS datasets were collected from various sources, currently representing over 1,000 diverse accessions for soybean, Arabidopsis, and maize individually. The main features of the Allele Catalog Tool include data query, visualization of results, categorical filtering, and download functions. Queries are performed from user input, and results are a tabular format of summary results by categorical description and genotype results of the alleles for each gene. The categorical information is specific to each species; additionally, available detailed meta-information is provided in modal popups. The genotypic information contains the variant positions, reference or alternate genotypes, the functional effect classes, and the amino-acid changes of each accession. Besides that, the results can also be downloaded for other research purposes.
The Allele Catalog Tool is a web-based tool that currently supports three species: soybean, Arabidopsis, and maize. The Soybean Allele Catalog Tool is hosted on the SoyKB website ( https://soykb.org/SoybeanAlleleCatalogTool/ ), while the Allele Catalog Tool for Arabidopsis and maize is hosted on the KBCommons website ( https://kbcommons.org/system/tools/AlleleCatalogTool/Zmays and https://kbcommons.org/system/tools/AlleleCatalogTool/Athaliana ). Researchers can use this tool to connect variant alleles of genes with meta-information of species.
当今测序技术的进步使得大量全基因组重测序（WGRS）数据可供公开使用。然而，如果没有进一步的配置，利用这些 WGRS 数据进行研究几乎是不可能的。为了解决这个问题，我们的研究小组开发了一个交互式等位基因目录工具，使研究人员能够探索超过 1000 个重测序品系中每个大豆、拟南芥和玉米的编码区域等位基因变异。
等位基因目录工具最初是基于大豆基因组数据和资源设计的。等位基因目录数据集是使用我们的变异调用管道（SnakyVC）和等位基因目录管道（AlleleCatalog）生成的。变异调用管道是为了并行处理原始测序reads 以生成变体调用格式（VCF）文件而开发的，而等位基因目录管道则采用 VCF 文件来执行 imputations、功能效应预测，并为每个基因组装等位基因，以生成经过校对的等位基因目录数据集。这两个管道都被用来生成数据面板（VCF 文件和等位基因目录文件），其中 WGRS 数据集的品系来自各种来源，目前代表每个大豆、拟南芥和玉米的 1000 多个不同品系。等位基因目录工具的主要功能包括数据查询、结果可视化、分类筛选和下载功能。查询是从用户输入执行的，结果是按分类描述和每个基因的等位基因基因型结果的表格格式。分类信息是特定于每个物种的；此外，还提供了模态弹出窗口中的可用详细元信息。基因型信息包含每个品系的变异位置、参考或替代基因型、功能效应类别和氨基酸变化。除此之外，还可以为其他研究目的下载结果。
等位基因目录工具是一个基于网络的工具，目前支持三种物种：大豆、拟南芥和玉米。大豆等位基因目录工具托管在 SoyKB 网站（https://soykb.org/SoybeanAlleleCatalogTool/）上，而拟南芥和玉米的等位基因目录工具托管在 KBCommons 网站上（https://kbcommons.org/system/tools/AlleleCatalogTool/Zmays 和 https://kbcommons.org/system/tools/AlleleCatalogTool/Athaliana）。研究人员可以使用该工具将基因的变异等位基因与物种的元信息连接起来。
