Abstract
DNA replication is one of the most basic processes in all three domains of cellular life. With the advent of the post-genomic era, the increasing number of complete archaeal genomes has created an opportunity for exploration of the molecular mechanisms for initiating cellular DNA replication by in vivo experiments as well as in silico analysis. However, the location of replication origins (oriCs) in many sequenced archaeal genomes remains unknown. We present a web-based tool Ori-Finder 2 to predict oriCs in the archaeal genomes automatically, based on the integrated method comprising the analysis of base composition asymmetry using the Z-curve method, the distribution of origin recognition boxes identified by FIMO tool, and the occurrence of genes frequently close to oriCs. The web server is also able to analyze the unannotated genome sequences by integrating with gene prediction pipelines and BLAST software for gene identification and function annotation. The result of the predicted oriCs is displayed as an HTML table, which offers an intuitive way to browse the result in graphical and tabular form. The software presented here is accurate for the genomes with single oriC, but it does not necessarily find all the origins of replication for the genomes with multiple oriCs. Ori-Finder 2 aims to become a useful platform for the identification and analysis of oriCs in the archaeal genomes, which would provide insight into the replication mechanisms in archaea. The web server is freely available at http://tubic.tju.edu.cn/Ori-Finder2/.
Highlights
DNA replication is one of the essential and conserved features among all three domains of life
With the knowledge of oriCs in the archaeal genomes, we present an online tool, Ori-Finder 2, to identify the oriCs in the archaeal genomes, based on the integrated method comprising the analysis of base composition asymmetry using the Z-curve method, the distribution of origin recognition boxes (ORBs) elements identified by Find Individual Motif Occurrences (FIMO) tool, and the occurrence of genes frequently close to replication origins, which is available at http://tubic.tju.edu.cn/Ori-Finder2/
Pyrococcus abyssi is a classical model of DNA replication in the archaeal organisms
Summary
DNA replication is one of the essential and conserved features among all three domains of life. The oriCs in archaea are located in the intergenic regions around the replication-related proteins and distributed with the origin recognition boxes (ORBs). The ORB motifs are the conserved sequences and recognition sites for the Orc1/Cdc initiation proteins (Barry and Bell, 2006). G-stretches are observed at the end of ORBs. On the other hand, the origin binding proteins in archaea are homologous to the related eukaryotic Orc1/Cdc proteins, and some archaea could adopt more than one oriC to initiate DNA replication. With the increasing availability of complete archaeal genomes, identification of their oriCs would provide further insight into the mechanism of DNA replication in archaea and reveal the evolutionary history between bacteria and eukaryotes (Barry and Bell, 2006; Wu et al, 2014b)
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