fivepseq

fivepseq analyzes distributions of 5' endpoints from RNA sequencing datasets capturing 5' monophosphorylated RNAs, including 5PSeq, PARE-seq, GMUC and ribosome profiling, to characterize RNA decay and ribosome dynamics.

Key Features:

• Supported datasets: Supports 5' monophosphorylated RNA sequencing datasets including 5PSeq, PARE-seq, GMUC, and ribosome profiling.
• Visualization of 5' endpoints: Visualizes 5' endpoint distributions and degradome profiles to reveal positional patterns of RNA cleavage and protection.
• Metagene and gene-specific analysis: Performs global metagene analyses and gene-level analyses to examine translational features across transcripts.
• Codon-specific pause analysis: Detects and quantifies codon-specific ribosome pauses and stalling events.
• Frameshift identification: Identifies frameshifts linked to ribosome stalling.
• Motif and termination-level protection analysis: Detects motif-specific ribosome protection and increased ribosome protection at termination sites.

Scientific Applications:

• Ribosome dynamics in eukaryotes: Characterizes ribosome positioning and 5'-3' co-translational degradation dynamics in vivo.
• Gene-specific investigations: Analyzes gene-specific ribosome pauses such as those observed in S. cerevisiae following eIF5A depletion and associated frameshifts.
• Developmental insights in plants: Profiles motif-specific ribosome protection and termination-associated protection across developmental stages in Arabidopsis thaliana.

Methodology:

Provides reproducible computational analysis of 5'P degradome data.