Department of Physics, School of Science, Tianjin University.
Department of Physics, School of Science, and the Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University.
Brief Bioinform. 2021 May 20;22(3). doi: 10.1093/bib/bbaa182.
DNA replication is a fundamental process in all organisms; this event initiates at sites termed origins of replication. The characteristics of eukaryotic replication origins are best understood in Saccharomyces cerevisiae. For this species, origin prediction algorithms or web servers have been developed based on the sequence features of autonomously replicating sequences (ARSs). However, their performances are far from satisfactory. By utilizing the Z-curve methodology, we present a novel pipeline, Ori-Finder 3, for the computational prediction of replication origins in S. cerevisiae at the genome-wide level based solely on DNA sequences. The ARS exhibiting both an AT-rich stretch and ARS consensus sequence element can be predicted at the single-nucleotide level. For the identified ARSs in the S. cerevisiae reference genome, 83 and 60% of the top 100 and top 300 predictions matched the known ARS records, respectively. Based on Ori-Finder 3, we subsequently built a database of the predicted ARSs identified in more than a hundred S. cerevisiae genomes. Consequently, we developed a user-friendly web server including the ARS prediction pipeline and the predicted ARSs database, which can be freely accessed at http://tubic.tju.edu.cn/Ori-Finder3.
DNA 复制是所有生物的基本过程；这个事件从称为复制起点的位点开始。真核生物复制起点的特征在酿酒酵母中得到了最好的理解。对于该物种，已经基于自主复制序列（ARS）的序列特征开发了起源预测算法或网络服务器。然而，它们的性能远不能令人满意。通过利用 Z 曲线方法，我们提出了一种新的管道 Ori-Finder 3，用于在全基因组水平上仅基于 DNA 序列计算预测酿酒酵母中的复制起点。表现出富含 AT 区域和 ARS 共识序列元件的 ARS 可以在单核苷酸水平上进行预测。对于酿酒酵母参考基因组中鉴定的 ARS，前 100 个和前 300 个预测中的 83%和 60%分别与已知的 ARS 记录匹配。基于 Ori-Finder 3，我们随后构建了一个包含一百多个酿酒酵母基因组中鉴定的预测 ARS 的数据库。因此，我们开发了一个用户友好的网络服务器，包括 ARS 预测管道和预测的 ARS 数据库，可在 http://tubic.tju.edu.cn/Ori-Finder3 上免费访问。
