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

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Single-molecule real-time (SMRT) Iso-Seq offers insights into full-length RNA isoforms.
• Comprehensive bioinformatics tools are needed for Iso-Seq data analysis.
• Existing tools may not cover the full spectrum of isoform analysis.

Purpose of the Study:

• To develop a one-stop solution for comprehensive Iso-Seq data analysis.
• To integrate Iso-Seq data with short-read sequencing for differential expression analysis.
• To enable gene annotation and correction using Iso-Seq data.

Main Methods:

• PRAPI analyzes alternative transcription initiation (ATI), alternative splicing (AS), alternative cleavage and polyadenylation (APA), natural antisense transcripts (NAT), and circular RNAs (circRNAs).
• Integrates Iso-Seq data with RNA-Seq or PAS-seq for differential expression analysis of NAT, AS, APA, and circRNAs.
• Supports gene annotation and correction of mis-annotated genes.

Main Results:

• PRAPI provides a comprehensive analysis of various RNA isoforms from Iso-Seq data.
• Enables differential expression analysis by combining Iso-Seq with short-read data.
• Facilitates gene annotation and correction, improving genomic databases.
• Generates high-quality vector graphics for visualization of Iso-Seq results.

Conclusions:

• PRAPI serves as a valuable, integrated tool for Iso-Seq bioinformatics analysis.
• It enhances the utility of Iso-Seq data for understanding transcriptomic complexity.
• The tool aids in gene discovery and annotation, contributing to more accurate genome representation.