The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F23%3A73622302" target="_blank" >RIV/61989592:15310/23:73622302 - isvavai.cz</a>

Result on the web

<a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-023-09161-3" target="_blank" >https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-023-09161-3</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1186/s12864-023-09161-3" target="_blank" >10.1186/s12864-023-09161-3</a>

Result language

angličtina

Original language name

The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis

Original language description

Background 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. Results 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. Conclusions 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, while the Allele Catalog Tool for Arabidopsis and maize is hosted on the KBCommons website. Researchers can use this tool to connect variant alleles of genes with meta-information of species.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

10608 - Biochemistry and molecular biology

Project

—

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2023

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

BMC GENOMICS

ISSN

1471-2164

e-ISSN

—

Volume of the periodical

24

Issue of the periodical within the volume

1

Country of publishing house

GB - UNITED KINGDOM

Number of pages

14

Pages from-to

"107-1"-"107-14"

UT code for WoS article

000948853400002

EID of the result in the Scopus database

2-s2.0-85150010861