utR.annotation

utR.annotation annotates genomic variants in untranslated regions (UTRs) to predict their potential effects on post-transcriptional regulation.

Key Features:

• Implementation: Implemented as an R package for annotating UTR variants.
• Species Compatibility: Supports human and mouse genomes.
• Input Formats: Accepts variant data in CSV and VCF formats.
• Translational Regulator Annotation: Identifies how variants may alter upstream open reading frames (uORFs), upstream Kozak sequences, and polyA signals.
• Translation Initiation Site Evaluation: Evaluates changes to the Kozak sequence at the annotated translation initiation site, start codon, and stop codon.
• Conservation Scores: Assesses conservation scores at variant positions.
• Ribosome Loading Predictions: Predicts changes in ribosome loading using empirical data models.

Scientific Applications:

• Functional Genomics Research: Annotates UTR variants to aid prediction of their impact on gene expression and post-transcriptional regulation.
• Comparative Genomics: Enables analyses across human and mouse to identify conserved regulatory mechanisms in UTRs.
• Precision Medicine: Highlights potentially deleterious UTR variants that may inform personalized therapeutic investigations.

Methodology:

Assesses changes to Kozak sequences, uORFs, upstream Kozak sequences, polyA signals, and conservation scores at variant positions, and integrates empirical data models to predict changes in ribosome loading.