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Ori-Finder 2022:A Comprehensive Web Server for Prediction and Analysis of Bacterial replication origins

Genomics, Proteomics & Bioinformatics 2022年第6期20卷 1207-1213页

作者： Mei-Jing Dong Hao Luo Feng Gao Department of Physics School of ScienceTianjin UniversityTianjin 300072China Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering(Ministry of Education) Tianjin UniversityTianjin 300072China SynBio Research Platform Collaborative Innovation Center of Chemical Science and Engineering(Tianjin)Tianjin 300072China

The replication of DNA is a complex biological process that is essential for *** 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 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 *** has facilitated large-scale data mining of functional elements in oriCs and strand-biased ***,we describe Ori-Finder 2022 with updated prediction framework,interactive visualization module,new analysis module,and user-friendly *** 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 *** interactive visualization module displays more genomic information related to oriCs and their functional *** analysis module includes regulatory protein annotation,repeat sequence discovery,homologous oriC search,and strand-biased *** redesigned interface provides additional customization options for oriC ***-Finder 2022 is freely available at http://***/Ori-Finder/and https://***/Ori-Finder/.

关键词： Bacteria DNA replication replication origin Z-curve DnaA-trio

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DNAskew:Statistical Analysis of Base Compositional Asymmetry and Prediction of replication Boundaries in the Genome Sequences

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Acta Biochimica et Biophysica Sinica 2004年第1期36卷 16-20页

作者： Xiang-Ru MA, Shao-Bo XIAO, Ai-Zhen GUO, Jian-Qiang LU, and Huan-Chun CHEN( Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China ) Laboratory of Animal Virology College of Veterinary Medicine Huazhong Agricultural University Wuhan 430070 China

Sueoka and Lobry declared respectively that, in the absence of bias between the two DNA strands for mutation and selection, the base composition within each strand should be A=T and C=G (this state is called Parity Rule type 2, PR2). However, the genome sequences of many bacteria, vertebrates and viruses showed asymmetries in base composition and gene direction. To determine the relationship of base composition skews with replication orientation, gene function, codon usage biases and phylogenetic evolution, in this paper a program called DNAskew was developed for the statistical analysis of strand asymmetry and codon composition bias in the DNA sequence. In addition, the program can also be used to predict the replication boundaries of genome sequences. The method builds on the fact that there are compositional asymmetries between the leading and the lagging strand for replication. DNAskew was written in Perl script language and implemented on the LINUX operating system. It works quickly with annotated

关键词： strand asymmetry base composition statistics analysis replication origin bioinformatics

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Regulation of eukaryotic DNA replication and nuclear structure

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Cell Research 1999年第3期9卷 163-170页

作者： WU JIA RUI(Shanghai Institute of Biochemistry, Chinese Academy ofSciences Shanghai 200031, China)e-mail: wwir@sunm.shcnc. ac. cn 1Shanghai Institute of Biochemistry Chinese Academy of Sciences Shanghai 200031 China e-mail: wujr@***

In eukaryote, nuclear structure is a key component forthe functions of eukaryotic cells. More and more evidencesshow that the nuclear structure plays important role in re-gulating DNA replication. The nuclear structure providesa physical barrier for the replication licensing, participatesin the decision where DNA replication initiates, and orga-nizes replication proteins as replication factory for DNAreplication. Through these works, new concepts on theregulation of DNA replication have emerged, which willbe discussed in this minireview.

关键词： DNA replication nuclear structure replication licensing replication origin replication factory

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Motif analysis in bacterial and eukaryotic replication origins

Motif analysis in bacterial and eukaryotic replication origi...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Chong Peng Hao Luo 高峰 Department of Physics Tianjin University

Background:replication of chromosomes is one of the central events in the cell cycle. DNA replication begins at a specific site,called an origin of replication,in all three domains of *** bacteria,replication initiates from a single replication origin,whereas replication initiates from many replication origins activated simultaneously at a specific time in the eukaryotic genome. Methods:Based on the Z-curve theory,with the means of comparative genomics,we have developed a web-based system Ori-Finder for finding oriCs in bacterial genomes with high accuracy and reliability,and the predicted oriC regions in over 1,000 bacterial genomes have been organized into an online database,***,we have also constructed a Database of Eukaryotic ORIs(DeOri),which contains over ten thousand Eukaryotic ORIs identified by genome-wide analyses currently ***-based sequence analysis tools, the MEME Suite,were used to discover motifs in the replication origins. Results:Analyzing sequence motifs in the replication origins identified by MEME Suite, we found the relationships between the DnaA boxes and taxonomic levels or genomic GC *** addition,we found the AT-rich motifs are enriched in the replication origins. Conclusions:The discovered motifs in the replication origins will be useful to develop algorithms to predict replication origins,and further analysis of the conserved motifs within the origins will be helpful to reveal the regulatory mechanisms of the initiation step in DNA replication.

关键词： replication origin motif analysis MEME Suite AT-rich motif

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