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Paralog Explorer: a resource for mining information about paralogs in common research organisms
Computational and Structural Biotechnology Journal ( IF 4.4 ) Pub Date : 2022-11-24 , DOI: 10.1016/j.csbj.2022.11.041
Yanhui Hu 1, 2 , Ben Ewen-Campen 1 , Aram Comjean 1, 2 , Jonathan Rodiger 1, 2 , Stephanie E Mohr 1, 2 , Norbert Perrimon 1, 2, 3
Affiliation  

Paralogs are genes which arose via gene duplication, and when such paralogs retain overlapping or redundant function, this poses a challenge to functional genetics research. Recent technological advancements have made it possible to systematically probe gene function for redundant genes using dual or multiplex gene perturbation, and there is a need for a simple bioinformatic tool to identify putative paralogs of a gene(s) of interest. We have developed Paralog Explorer (https://www.flyrnai.org/tools/paralogs/), an online resource that allows researchers to quickly and accurately identify candidate paralogous genes in the genomes of the model organisms D. melanogaster, C. elegans, D. rerio, M. musculus, and H. sapiens. Paralog Explorer deploys an effective between-species ortholog prediction software, DIOPT, to analyze within-species paralogs. Paralog Explorer allows users to identify candidate paralogs, and to navigate relevant databases regarding gene co-expression, protein-protein and genetic interaction, as well as gene ontology and phenotype annotations. Altogether, this tool extends the value of current ortholog prediction resources by providing sophisticated features useful for identification and study of paralogous genes.



中文翻译:


Paralog Explorer:用于挖掘常见研究生物体中旁系同源信息的资源



旁系同源物是通过基因复制产生的基因,当此类旁系同源物保留重叠或冗余功能时,这对功能遗传学研究提出了挑战。最近的技术进步使得使用双重或多重基因扰动系统地探测冗余基因的基因功能成为可能,并且需要一种简单的生物信息学工具来识别感兴趣基因的假定旁系同源物。我们开发了 Paralog Explorer (https://www.flyrnai.org/tools/paralogs/),这是一种在线资源,使研究人员能够快速准确地识别模式生物D. melanogaster、C. elegans基因组中的候选旁系同源基因、 D. rerio、M. musculusH. sapiens 。 Paralog Explorer 部署了有效的种间直系同源预测软件 DIOPT 来分析种内旁系同源。 Paralog Explorer 允许用户识别候选旁系同源物,并浏览有关基因共表达、蛋白质-蛋白质和遗传相互作用以及基因本体和表型注释的相关数据库。总而言之,该工具通过提供可用于识别和研究旁系同源基因的复杂功能,扩展了当前直向同源预测资源的价值。

更新日期:2022-11-25
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