Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
Universitat Pompeu Fabra, Barcelona, Spain.
Methods Mol Biol. 2022;2537:97-128. doi: 10.1007/978-1-0716-2521-7_7.
Alternative splicing (AS) can vastly expand animal transcriptomes and proteomes. Two main open questions in the field are how AS is regulated across cell/tissue types and disease, and what roles different AS events play. To facilitate AS research, we have created the computational VastDB framework, which comprises a series of complementary software and resources that we describe in this chapter. The VastDB framework is especially designed to aid biomedical researchers without a strong computational background. It offers tools and resources to: (a) quantify AS and identify differentially spliced AS events using RNA-seq data (vast-tools), (b) perform multiple genomic and sequence analyses for investigating AS events (Matt), (c) identify AS events with genomic and regulatory conservation among species (ExOrthist), and (d) help with the biological interpretation of the results, and, ultimately, with the identification of interesting AS events to design wet-lab experiments (VastDB and PastDB).
可变剪接 (AS) 可以极大地扩展动物的转录组和蛋白质组。该领域的两个主要问题是 AS 如何在细胞/组织类型和疾病中被调控，以及不同的 AS 事件扮演何种角色。为了促进 AS 研究，我们创建了计算性的 VastDB 框架，该框架包括一系列互补的软件和资源，我们将在本章中进行介绍。VastDB 框架是专门为没有强大计算背景的生物医学研究人员设计的。它提供了工具和资源，用于：(a) 使用 RNA-seq 数据定量 AS 和识别差异剪接的 AS 事件（vast-tools），(b) 进行多种基因组和序列分析以研究 AS 事件（Matt），(c) 在物种间识别具有基因组和调控保守性的 AS 事件（ExOrthist），以及 (d) 帮助对结果进行生物学解释，并最终识别有趣的 AS 事件以设计湿实验（VastDB 和 PastDB）。
