PRAPI：Iso-Seq 的转录后调控分析管道。

PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq.

机构信息

Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Department of Plant Pathology and Microbiology, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA.

出版信息

Bioinformatics. 2018 May 1;34(9):1580-1582. doi: 10.1093/bioinformatics/btx830.

DOI:10.1093/bioinformatics/btx830

PMID:29280994

Abstract

SUMMARY

The single-molecule real-time (SMRT) isoform sequencing (Iso-Seq) based on Pacific Bioscience (PacBio) platform has received increasing attention for its ability to explore full-length isoforms. Thus, comprehensive tools for Iso-Seq bioinformatics analysis are extremely useful. Here, we present a one-stop solution for Iso-Seq analysis, called PRAPI to analyze alternative transcription initiation (ATI), alternative splicing (AS), alternative cleavage and polyadenylation (APA), natural antisense transcripts (NAT), and circular RNAs (circRNAs) comprehensively. PRAPI is capable of combining Iso-Seq full-length isoforms with short read data, such as RNA-Seq or polyadenylation site sequencing (PAS-seq) for differential expression analysis of NAT, AS, APA and circRNAs. Furthermore, PRAPI can annotate new genes and correct mis-annotated genes when gene annotation is available. Finally, PRAPI generates high-quality vector graphics to visualize and highlight the Iso-Seq results.

AVAILABILITY AND IMPLEMENTATION

The Dockerfile of PRAPI is available at http://www.bioinfor.org/tool/PRAPI.

CONTACT

lfgu@fafu.edu.cn.

摘要

基于 Pacific Bioscience（PacBio）平台的单分子实时（SMRT）异构体测序（Iso-Seq）因其能够探索全长异构体而受到越来越多的关注。因此，用于 Iso-Seq 生物信息学分析的综合工具非常有用。在这里，我们提出了一种用于 Iso-Seq 分析的一站式解决方案，称为 PRAPI，用于全面分析选择性转录起始（ATI）、选择性剪接（AS）、选择性剪接和多聚腺苷酸化（APA）、天然反义转录物（NAT）和环状 RNA（circRNA）。PRAPI 能够将 Iso-Seq 全长异构体与短读数据（如 RNA-Seq 或多聚腺苷酸化位点测序（PAS-seq））结合使用，用于 NAT、AS、APA 和 circRNA 的差异表达分析。此外，当基因注释可用时，PRAPI 可以注释新基因并纠正错误注释的基因。最后，PRAPI 生成高质量的矢量图形，以可视化和突出显示 Iso-Seq 结果。