CentroidFold

CentroidFold predicts RNA secondary structures to provide accurate secondary-structure models for analysis of non-coding RNAs and conserved structural elements.

Key Features:

• Input Flexibility: Accepts single RNA sequences (FASTA or plain text) and multiple sequence alignments in CLUSTAL-W format.
• Comprehensive Output: Produces base-pair notation and graphical representations of predicted secondary structures, with graphical output available as PDF.
• Common Structure Prediction: Predicts a common secondary structure from multiple sequence alignments to identify conserved structural elements.
• High Accuracy: Implements the original CentroidFold prediction software, reported to achieve superior accuracy in benchmark tests.

Scientific Applications:

• ncRNA analysis: Enables analysis of non-coding RNAs (ncRNAs) by providing predicted secondary-structure models for functional and interaction studies.
• Comparative and evolutionary studies: Supports comparative analyses across sequences and identification of evolutionarily conserved RNA structures.
• Molecular biology, genetics, and bioinformatics research: Applicable to exploratory studies of individual RNA molecules and comparative studies to assess functional diversity.

Methodology:

Uses the original CentroidFold prediction engine to compute secondary structures from single sequences or multiple alignments (FASTA, CLUSTAL-W), outputting base-pair notation and graphical representations and predicting a common secondary structure for alignments.