RegRNA

RegRNA: Regulatory RNA Motif Identification and Annotation

RegRNA identifies and annotates regulatory RNA motifs within mRNA sequences by detecting sequence and structural homologs of known regulatory RNA elements involved in transcriptional and post-transcriptional gene regulation.

Key Features:

• Motif Detection: Identifies 5'-UTR and 3'-UTR motifs, splicing-related motifs, transcriptional regulation motifs, riboswitches, splicing donor and acceptor sites, inverted repeats, and miRNA target sites.
• Database Integration: Incorporates data from UTRdb, TRANSFAC, Alternative Splicing Database (ASD), and miRBase for regulatory element annotation.
• Sequence and Structural Homology Analysis: Detects regulatory RNA elements based on sequence similarity and predicted secondary structure features.

Scientific Applications:

• Functional Genomics: Characterizes regulatory RNA elements influencing gene expression at transcriptional and post-transcriptional levels.
• Molecular Biology: Analyzes structural and functional roles of RNA motifs in mRNA processing and regulation.
• Biotechnology: Supports design and evaluation of synthetic RNA sequences with regulatory functions.

Methodology:

RegRNA integrates computational programs to analyze mRNA sequences for conserved sequence motifs and secondary structure features, enabling identification of regulatory RNA elements through homology-based comparison against curated databases including UTRdb, TRANSFAC, ASD, and miRBase.