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G4Bank:一个经实验鉴定的DNA G-四链体序列数据库。

G4Bank: A database of experimentally identified DNA G-quadruplex sequences.

作者信息

Zhong Hong-Sheng, Dong Mei-Jing, Gao Feng

机构信息

Department of Physics, School of Science, Tianjin University, Tianjin, 300072, China.

Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.

出版信息

Interdiscip Sci. 2023 Sep;15(3):515-523. doi: 10.1007/s12539-023-00577-9. Epub 2023 Jun 30.

Abstract

G-quadruplex (G4), a non-canonical nucleic acid structure, has been suggested to play a key role in important cellular processes including transcription, replication and cancer development. Recently, high-throughput sequencing approaches for G4 detection have provided a large amount of experimentally identified G4 data that reveal genome-wide G4 landscapes and enable the development of new methods for predicting potential G4s from sequences. Although several existing databases provide G4 experimental data and relevant biological information from different perspectives, there is no dedicated database to collect and analyze DNA G4 experimental data genome-widely. Here, we constructed G4Bank, a database of experimentally identified DNA G-quadruplex sequences. A total of 6,915,983 DNA G4s were collected from 13 organisms, and state-of-the-art prediction methods were performed to filter and analyze the G4 data. Therefore, G4Bank will facilitate users to access comprehensive G4 experimental data and enable sequence feature analysis of G4 for further investigation. The database of the experimentally identified DNA G-quadruplex sequences can be accessed at http://tubic.tju.edu.cn/g4bank/ .

摘要

G-四链体(G4)是一种非经典核酸结构,已被认为在包括转录、复制和癌症发展等重要细胞过程中发挥关键作用。最近,用于G4检测的高通量测序方法提供了大量经实验鉴定的G4数据,这些数据揭示了全基因组的G4图谱,并使得开发从序列预测潜在G4的新方法成为可能。尽管现有的几个数据库从不同角度提供了G4实验数据和相关生物学信息,但尚无专门用于全基因组收集和分析DNA G4实验数据的数据库。在此,我们构建了G4Bank,一个经实验鉴定的DNA G-四链体序列数据库。共从13种生物中收集了6915983个DNA G4,并采用最先进的预测方法对G4数据进行过滤和分析。因此,G4Bank将方便用户获取全面的G4实验数据,并能够对G4进行序列特征分析以进一步研究。经实验鉴定的DNA G-四链体序列数据库可在http://tubic.tju.edu.cn/g4bank/ 访问。

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