{"title":"Ori-Finder 2022:用于预测和分析细菌复制起源的综合Web服务器","authors":"Mei-Jing Dong , Hao Luo , Feng Gao","doi":"10.1016/j.gpb.2022.10.002","DOIUrl":null,"url":null,"abstract":"<div><p>The replication of DNA is a complex biological process that is essential for life. Bacterial <strong>DNA replication</strong> is initiated at genomic loci referred to as <strong>replication origins</strong> (<em>oriC</em>s). Integrating the <strong>Z-curve</strong> method, DnaA box distribution, and comparative genomic analysis, we developed a web server to predict bacterial <em>oriC</em>s in 2008 called Ori-Finder, which is helpful to clarify the characteristics of bacterial <em>oriC</em>s. The <em>oriC</em>s 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 <em>oriC</em>s. This has facilitated large-scale data mining of functional elements in <em>oriC</em>s 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 <em>oriC</em>s are integrated into the updated framework, which has also been redesigned to predict <em>oriC</em>s in draft genomes. The interactive visualization module displays more genomic information related to <em>oriC</em>s and their functional elements. The analysis module includes regulatory protein annotation, repeat sequence discovery, homologous <em>oriC</em> search, and strand-biased analyses. The redesigned interface provides additional customization options for <em>oriC</em> prediction. Ori-Finder 2022 is freely available at <span>http://tubic.tju.edu.cn/Ori-Finder/</span><svg><path></path></svg> and <span>https://tubic.org/Ori-Finder/</span><svg><path></path></svg>.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"20 6","pages":"Pages 1207-1213"},"PeriodicalIF":11.5000,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10225481/pdf/","citationCount":"14","resultStr":"{\"title\":\"Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins\",\"authors\":\"Mei-Jing Dong , Hao Luo , Feng Gao\",\"doi\":\"10.1016/j.gpb.2022.10.002\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>The replication of DNA is a complex biological process that is essential for life. Bacterial <strong>DNA replication</strong> is initiated at genomic loci referred to as <strong>replication origins</strong> (<em>oriC</em>s). Integrating the <strong>Z-curve</strong> method, DnaA box distribution, and comparative genomic analysis, we developed a web server to predict bacterial <em>oriC</em>s in 2008 called Ori-Finder, which is helpful to clarify the characteristics of bacterial <em>oriC</em>s. The <em>oriC</em>s 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 <em>oriC</em>s. This has facilitated large-scale data mining of functional elements in <em>oriC</em>s 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 <em>oriC</em>s are integrated into the updated framework, which has also been redesigned to predict <em>oriC</em>s in draft genomes. The interactive visualization module displays more genomic information related to <em>oriC</em>s and their functional elements. The analysis module includes regulatory protein annotation, repeat sequence discovery, homologous <em>oriC</em> search, and strand-biased analyses. The redesigned interface provides additional customization options for <em>oriC</em> prediction. Ori-Finder 2022 is freely available at <span>http://tubic.tju.edu.cn/Ori-Finder/</span><svg><path></path></svg> and <span>https://tubic.org/Ori-Finder/</span><svg><path></path></svg>.</p></div>\",\"PeriodicalId\":12528,\"journal\":{\"name\":\"Genomics, Proteomics & Bioinformatics\",\"volume\":\"20 6\",\"pages\":\"Pages 1207-1213\"},\"PeriodicalIF\":11.5000,\"publicationDate\":\"2022-12-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10225481/pdf/\",\"citationCount\":\"14\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genomics, Proteomics & Bioinformatics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1672022922001309\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genomics, Proteomics & Bioinformatics","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1672022922001309","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
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/.
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.