PRAPI

PRAPI analyzes post-transcriptional regulation using full-length isoform sequencing (Iso-Seq) data from PacBio single-molecule real-time (SMRT) platforms and integrates complementary short-read datasets (RNA-Seq, polyadenylation site sequencing (PAS-seq)) to detect alternative transcription initiation (ATI), alternative splicing (AS), alternative cleavage and polyadenylation (APA), natural antisense transcripts (NAT), and circular RNAs (circRNAs) and to annotate or correct gene models.

Key Features:

• Comprehensive analysis of post-transcriptional events: Analyzes alternative transcription initiation (ATI), alternative splicing (AS), alternative cleavage and polyadenylation (APA), natural antisense transcripts (NAT), and circular RNAs (circRNAs) from full-length Iso-Seq isoforms.
• Integration with short-read data: Integrates Iso-Seq full-length isoforms with short-read RNA-Seq and polyadenylation site sequencing (PAS-seq) to support differential expression analysis across post-transcriptional events.
• Gene annotation and correction: Annotates novel genes and corrects mis-annotated gene models when reference gene annotation data are available.
• Visualization outputs: Generates vector graphics to visualize Iso-Seq results and associated post-transcriptional events.

Scientific Applications:

• Profiling post-transcriptional regulation: Characterizes transcriptomic diversity and regulation at the post-transcriptional level using full-length isoform resolution.
• Discovery of novel transcripts and variants: Identifies novel transcripts, splice variants, and regulatory elements that may be missed by short-read sequencing technologies.
• Differential analysis of events: Enables differential expression analysis of ATI, AS, APA, NAT, and circRNAs by combining Iso-Seq with RNA-Seq or PAS-seq.

Methodology:

Integration of Iso-Seq full-length isoforms with complementary short-read datasets (RNA-Seq, PAS-seq) for combined analysis of post-transcriptional events and gene model annotation/correction.