ArticleBMC genomics2023
The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis.
Article in BMC genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed.
- SorghumHub: featuring the next phase for the KBCommons web portal with new molecular biology features.BMC genomics · 2026Article
- Molecular polymorphisms that underlie trait variation in crops: Lessons learned from soybean.The plant genome · 2026Review
- Genetic diversity analysis of North Dakota public soybean breeding program cultivars.Scientific reports · 2026Article
- Elevated Soybean Seed Oil Phenotype Associated with a Single Nucleotide Polymorphism inPlants (Basel, Switzerland) · 2025Article
- Dissecting seed composition QTL from wild soybean: fine-mapping, candidate gene identification, and evaluation of introgression effects on agronomic performance.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Factors underlying a latitudinal gradient in the S/G lignin monomer ratio in natural poplar variants.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Allele-tagged TaqManMolecular biology reports · 2024Article
- Soybean genomics research community strategic plan: A vision for 2024-2028.The plant genome · 2024Article
- Loss-of-function of an α-SNAP gene confers resistance to soybean cyst nematode.Nature communications · 2023Article
- Cataloging SCN resistance loci in North American public soybean breeding programs.Frontiers in plant science · 2023Article
- Natural and artificial selection of multiple alleles revealed through genomic analyses.Frontiers in genetics · 2023Article
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Abstract
backgroundThe 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.
resultsThe 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.
conclusionsThe 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.
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