大型比较动物 MicroRNA 数据集的自动整理。

Automatic curation of large comparative animal MicroRNA datasets.

机构信息

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, D-04107 Leipzig, Germany.

Doctoral School of Science and Technology, Center for Biotechnology Research, Lebanese University, Hadath Campus, Beirut, Lebanon.

出版信息

Bioinformatics. 2019 Nov 1;35(22):4553-4559. doi: 10.1093/bioinformatics/btz271.

DOI:10.1093/bioinformatics/btz271

PMID:30993337

Abstract

MOTIVATION

MicroRNAs form an important class of RNA regulators that has been studied extensively. The miRBase and Rfam database provide rich, frequently updated information on both pre-miRNAs and their mature forms. These data sources, however, rely on individual data submission and thus are neither complete nor consistent in their coverage across different miRNA families. Quantitative studies of miRNA evolution therefore are difficult or impossible on this basis.

RESULTS

We present here a workflow and a corresponding implementation, MIRfix, that automatically curates miRNA datasets by improving alignments of their precursors, the consistency of the annotation of mature miR and miR* sequence, and the phylogenetic coverage. MIRfix produces alignments that are comparable across families and sets the stage for improved homology search as well as quantitative analyses.

AVAILABILITY AND IMPLEMENTATION

MIRfix can be downloaded from https://github.com/Bierinformatik/MIRfix.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

动机

MicroRNAs 是一类重要的 RNA 调节剂，已经得到了广泛的研究。miRBase 和 Rfam 数据库提供了丰富的、经常更新的关于前体 miRNA 和它们的成熟形式的信息。然而，这些数据源依赖于单个数据提交，因此在不同 miRNA 家族的覆盖范围上既不完整也不一致。因此，基于这些数据基础，miRNA 进化的定量研究是困难的或不可能的。