SoMarker: a genetic marker searching tool for Caenorhabditis elegans.

IF 2.1 3区生物学 Q3 GENETICS & HEREDITY G3: Genes|Genomes|Genetics Pub Date : 2024-10-07 DOI:10.1093/g3journal/jkae197

Chuan-Yang Dai, Haobo Zhang, Steven Zuryn

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Abstract

Caenorhabditis elegans is one of the most popular model organisms used to genetically dissect complex biological phenomena. One common technique used routinely in the C. elegans laboratory is the generation of strains carrying combinations of genetic mutations via classical genetic crosses. Here, we have developed a simple and convenient application to quickly identify useful genetic markers (phenotypical and fluorescent) and their chromosomal positions to aid in the development of genetic cross strategies. The user-friendly software identifies and prioritizes markers with the least genetic distance to a gene of interest, as well as displays the strain name, ease of scoring, nature of the marker (fluorescent transgene or phenotypic information), mating efficiency, and number of available alleles. In addition, recombination frequencies between the gene of interest and each genetic marker are calculated automatically. The application, called "SoMarker," is designed for both MacOS and Windows environments and is available to freely download and modify through open-source software.

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SoMarker：用于秀丽隐杆线虫的遗传标记搜索工具。

秀丽隐杆线虫（Caenorhabditis elegans，简称 C.elegans）是用于从遗传学角度剖析复杂生物现象的最常用模式生物之一。elegans 实验室常规使用的一项常用技术是通过经典遗传杂交产生携带基因突变组合的品系。在此，我们开发了一款简单方便的应用程序，用于快速识别有用的遗传标记（表型和荧光）及其染色体位置，以帮助制定遗传杂交策略。这款用户友好型软件可识别与相关基因遗传距离最小的标记，并将其排序，还可显示品系名称、评分难易程度、标记性质（荧光转基因或表型信息）、交配效率和可用等位基因数量。此外，还会自动计算相关基因与每个遗传标记之间的重组频率。该应用程序名为 "SoMarker"，设计用于 MacOS 和 Windows 环境，可通过开源软件免费下载和修改。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

G3: Genes|Genomes|Genetics GENETICS & HEREDITY-

CiteScore

5.10

自引率

3.80%

发文量

305

审稿时长

3-8 weeks

期刊介绍： G3: Genes, Genomes, Genetics provides a forum for the publication of high‐quality foundational research, particularly research that generates useful genetic and genomic information such as genome maps, single gene studies, genome‐wide association and QTL studies, as well as genome reports, mutant screens, and advances in methods and technology. The Editorial Board of G3 believes that rapid dissemination of these data is the necessary foundation for analysis that leads to mechanistic insights. G3, published by the Genetics Society of America, meets the critical and growing need of the genetics community for rapid review and publication of important results in all areas of genetics. G3 offers the opportunity to publish the puzzling finding or to present unpublished results that may not have been submitted for review and publication due to a perceived lack of a potential high-impact finding. G3 has earned the DOAJ Seal, which is a mark of certification for open access journals, awarded by DOAJ to journals that achieve a high level of openness, adhere to Best Practice and high publishing standards.