pAliKiss

pAliKiss: RNA secondary structure prediction with pseudoknots in multiple sequence alignments

pAliKiss predicts RNA secondary structures within fixed multiple sequence alignments using abstract shape analysis, including pseudoknotted configurations up to kissing hairpin motifs.

Key Features:

• Integration with RNA Structure Tools: Integrates RNAshapes, RNAalishapes, pknotsRG, and pKiss to enable combined analysis of RNA secondary structures and pseudoknots.
• Pseudoknot Prediction: Performs abstract shape analysis on RNA structures containing pseudoknots up to the complexity of kissing hairpin motifs.
• Kissing Hairpin Motif Detection: Predicts kissing hairpin motifs from aligned RNA sequences.
• Abstract Shape Analysis: Extracts representative structural features from the RNA folding space rather than restricting prediction to minimum free energy structures.

Scientific Applications:

• Regulatory RNA Analysis: Identifies pseudoknotted and kissing hairpin structures in viral genomes and riboswitches to study RNA-mediated regulatory mechanisms.
• Comparative RNA Structure Analysis: Analyzes structural conservation and diversity across aligned RNA sequences from different species or conditions.

Methodology:

pAliKiss applies abstract shape analysis to the folding space of RNA sequences within fixed multiple sequence alignments and incorporates algorithms from RNAshapes, RNAalishapes, pknotsRG, and pKiss to predict pseudoknotted secondary structures, including kissing hairpin motifs.