PLAST-ncRNA

PLAST-ncRNA detects distant homologs of non-coding RNA (ncRNA) sequences in genomic sequences using a local alignment approach based on partition function posterior probabilities.

Key Features:

• Alignment Algorithm: Uses an alignment algorithm based on partition function posterior probabilities optimized for local alignments to detect distantly similar ncRNA sequences, including those embedded within large genomes.
• Hit Scoring and Thresholding: Produces a list of alignment hits scored by posterior probabilities and filters hits that surpass a predefined mean posterior probability threshold.
• Visualization of Posterior-Probability Regions: Provides alignment outputs that list detected hits and highlight regions within each local alignment that exhibit high posterior probabilities via the integrated PLAST alignment viewer.

Scientific Applications:

• ncRNA discovery: Identification of distantly related ncRNA homologs within genomic sequences.
• Evolutionary analysis: Comparative studies of ncRNA conservation and divergence across genomes.
• Functional annotation: Annotation of genomic regions by locating putative ncRNA elements based on local-alignment evidence.
• Regulatory element exploration: Detection and characterization of regulatory non-coding RNA elements within complex genomic contexts.

Methodology:

Local alignments are computed using an algorithm based on partition function posterior probabilities; hits are reported when their mean posterior probability exceeds a predefined threshold, and alignment regions with high posterior probabilities are highlighted for inspection.