RNAcode

RNAcode identifies evolutionarily conserved protein-coding regions in genomic sequences by detecting coding potential from comparative multiple sequence alignments using sequence conservation patterns.

Key Features:

• Automated homolog retrieval and preparation: Automates collection, selection, and preparation of homologous sequences from the NCBI database for downstream analysis.
• Single-sequence input: Operates from a single target nucleotide sequence to initiate homolog retrieval and analysis.
• RNAcode coding-sequence detector: Applies the RNAcode statistical detector to multiple sequence alignments to identify regions with coding potential.
• Automated pre- and post-processing: Integrates automated pre- and post-processing steps around the RNAcode analysis to prepare alignments and interpret results.
• Sensitivity for short coding sequences: Leverages sequence conservation patterns to improve detection accuracy for short coding sequences and conserved small peptides.

Scientific Applications:

• Conserved coding region identification: Detection of evolutionarily conserved protein-coding regions within genomic sequences.
• Short ORF and small peptide discovery: Identification of short coding sequences and conserved small peptides that may be missed by single-sequence methods.
• Exploration of unannotated regions and splicing variants: Analysis of unannotated genomic regions to uncover novel coding elements and potential alternative splicing events.

Methodology:

Accepts a single nucleotide sequence, retrieves homologous sequences from the NCBI database, constructs multiple sequence alignments, and analyzes these alignments with RNAcode to detect coding potential.