Ori-Finder 2022:用于预测和分析细菌复制起源的综合Web服务器

IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Genomics, Proteomics & Bioinformatics Pub Date : 2022-12-01 DOI:10.1016/j.gpb.2022.10.002
Mei-Jing Dong , Hao Luo , Feng Gao
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引用次数: 14

摘要

DNA的复制是一个复杂的生物过程,对生命至关重要。细菌DNA复制始于基因组位点,称为复制起点(oriCs)。2008年,我们将z曲线法、dna盒分布法和比较基因组分析相结合,开发了一个预测细菌oric的web服务器Ori-Finder,这有助于明确细菌oric的特征。使用Ori-Finder将数百个已测序细菌基因组的oric标注在基因组报告中,并将预测结果存入人工整理的oric数据库DoriC中。这为oric中功能元素的大规模数据挖掘和链偏分析提供了便利。在这里,我们用更新的预测框架、交互式可视化模块、新的分析模块和用户友好的界面来描述Ori-Finder 2022。更多的物种特异性指示基因和oric的功能元件被整合到更新的框架中,该框架也被重新设计以预测草稿基因组中的oric。交互式可视化模块显示更多与oric及其功能元件相关的基因组信息。分析模块包括调控蛋白注释、重复序列发现、同源oriC搜索和链偏分析。重新设计的界面为oriC预测提供了额外的自定义选项。Ori-Finder 2022可以在http://tubic.tju.edu.cn/Ori-Finder/和https://tubic.org/Ori-Finder/免费获得。
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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Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins

The replication of DNA is a complex biological process that is essential for life. Bacterial DNA replication is initiated at genomic loci referred to as replication origins (oriCs). Integrating the Z-curve method, DnaA box distribution, and comparative genomic analysis, we developed a web server to predict bacterial oriCs in 2008 called Ori-Finder, which is helpful to clarify the characteristics of bacterial oriCs. The oriCs of hundreds of sequenced bacterial genomes have been annotated in the genome reports using Ori-Finder and the predicted results have been deposited in DoriC, a manually curated database of oriCs. This has facilitated large-scale data mining of functional elements in oriCs and strand-biased analysis. Here, we describe Ori-Finder 2022 with updated prediction framework, interactive visualization module, new analysis module, and user-friendly interface. More species-specific indicator genes and functional elements of oriCs are integrated into the updated framework, which has also been redesigned to predict oriCs in draft genomes. The interactive visualization module displays more genomic information related to oriCs and their functional elements. The analysis module includes regulatory protein annotation, repeat sequence discovery, homologous oriC search, and strand-biased analyses. The redesigned interface provides additional customization options for oriC prediction. Ori-Finder 2022 is freely available at http://tubic.tju.edu.cn/Ori-Finder/ and https://tubic.org/Ori-Finder/.

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来源期刊
Genomics, Proteomics & Bioinformatics
Genomics, Proteomics & Bioinformatics Biochemistry, Genetics and Molecular Biology-Biochemistry
CiteScore
14.30
自引率
4.20%
发文量
844
审稿时长
61 days
期刊介绍: Genomics, Proteomics and Bioinformatics (GPB) is the official journal of the Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China. It aims to disseminate new developments in the field of omics and bioinformatics, publish high-quality discoveries quickly, and promote open access and online publication. GPB welcomes submissions in all areas of life science, biology, and biomedicine, with a focus on large data acquisition, analysis, and curation. Manuscripts covering omics and related bioinformatics topics are particularly encouraged. GPB is indexed/abstracted by PubMed/MEDLINE, PubMed Central, Scopus, BIOSIS Previews, Chemical Abstracts, CSCD, among others.
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