Ori-Finder 2022:A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins
- Author:
Dong MEI-JING
1
;
Luo HAO
;
Gao FENG
Author Information
1. Department of Physics,School of Science,Tianjin University,Tianjin 300072,China
- Keywords:
Bacteria;
DNA replication;
Replication origin;
Z-curve;
DnaA-trio
- From:
Genomics, Proteomics & Bioinformatics
2022;(6):1207-1213
- CountryChina
- Language:Chinese
-
Abstract:
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 character-istics 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 ele-ments in oriCs and strand-biased analysis.Here,we describe Ori-Finder 2022 with updated predic-tion 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 inter-active 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/.
