cirCodAn: A GHMM-based tool for accurate prediction of coding regions in circRNA.

3区 生物学 Q1 Biochemistry, Genetics and Molecular Biology
Denilson Fagundes Barbosa, Liliane Santana Oliveira, Pedro Gabriel Nachtigall, Rodolpho Valentini Junior, Nayane de Souza, Alexandre Rossi Paschoal, André Yoshiaki Kashiwabara
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引用次数: 0

Abstract

Studies focusing on characterizing circRNAs with the potential to translate into peptides are quickly advancing. It is helping to elucidate the roles played by circRNAs in several biological processes, especially in the emergence and development of diseases. While various tools are accessible for predicting coding regions within linear sequences, none have demonstrated accurate open reading frame detection in circular sequences, such as circRNAs. Here, we present cirCodAn, a novel tool designed to predict coding regions in circRNAs. We evaluated the performance of cirCodAn using datasets of circRNAs with strong translation evidence and showed that cirCodAn outperformed the other tools available to perform a similar task. Our findings demonstrate the applicability of cirCodAn to identify coding regions in circRNAs, which reveals the potential of use of cirCodAn in future research focusing on elucidating the biological roles of circRNAs and their encoded proteins. cirCodAn is freely available at https://github.com/denilsonfbar/cirCodAn.

cirCodAn:基于 GHMM 的工具,用于准确预测 circRNA 的编码区域。
对具有转化为多肽潜力的 circRNA 进行特征描述的研究正在迅速推进。这有助于阐明 circRNA 在多个生物过程中的作用,特别是在疾病的出现和发展中的作用。虽然有多种工具可用于预测线性序列中的编码区,但没有一种工具能准确检测环状序列(如 circRNA)中的开放阅读框。在这里,我们介绍了cirCodAn,这是一种用于预测circRNA编码区的新型工具。我们使用具有强有力翻译证据的 circRNA 数据集对 cirCodAn 的性能进行了评估,结果表明 cirCodAn 的性能优于其他可执行类似任务的工具。我们的研究结果证明了cirCodAn在识别circRNA编码区方面的适用性,这揭示了cirCodAn在未来重点阐明circRNA及其编码蛋白的生物学作用的研究中的应用潜力。cirCodAn可在https://github.com/denilsonfbar/cirCodAn 免费获取。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Advances in protein chemistry and structural biology
Advances in protein chemistry and structural biology BIOCHEMISTRY & MOLECULAR BIOLOGY-
CiteScore
7.40
自引率
0.00%
发文量
66
审稿时长
>12 weeks
期刊介绍: Published continuously since 1944, The Advances in Protein Chemistry and Structural Biology series has been the essential resource for protein chemists. Each volume brings forth new information about protocols and analysis of proteins. Each thematically organized volume is guest edited by leading experts in a broad range of protein-related topics.
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