PSI-MOUSE

PSI-MOUSE predicts pseudouridine (Ψ) sites within the mouse transcriptome by integrating sequence-derived features and 38 additional mouse genomic features to improve site identification and annotate posttranscriptional regulatory elements.

Key Features:

• Predictive Framework: Predicts pseudouridine sites in the mouse transcriptome using sequence-derived features combined with additional genomic features.
• Genomic Feature Integration: Incorporates 38 additional genomic features derived from the mouse genome to enhance prediction accuracy compared with sequence-only models.
• Posttranscriptional Regulation Annotation: Annotates predicted pseudouridine sites with RNA-binding protein (RBP) binding regions, miRNA-RNA interactions, and splicing sites.
• Experimental Validation Database: Maintains a database of 3282 experimentally validated mouse pseudouridine sites with customized query functions.

Scientific Applications:

• RNA modification mapping: Enables identification and mapping of pseudouridine sites across the mouse transcriptome.
• Functional characterization: Supports investigation of the biological functions and regulatory roles of pseudouridine in mouse RNA.
• Cross-species prediction advancement: Demonstrates integration of genomic features that can inform prediction approaches beyond human models to other species.

Methodology:

Predicts pseudouridine sites by combining sequence-derived features with 38 mouse genomic features, annotates predicted sites with RBP binding regions, miRNA-RNA interactions, and splicing sites, and organizes 3282 experimentally validated mouse pseudouridine sites in a queryable database.