SPARCS

SPARCS analyzes secondary-structure profiles of protein-coding regions in mRNAs to identify structured and unstructured regions whose RNA secondary structures may encode functional elements affecting post-transcriptional regulation such as splicing, localization, and translation.

Key Features:

• Secondary-structure profiling: Analyzes secondary-structure profiles of protein-coding regions within mRNAs.
• Sequence-preserving uniform sampling: Uniformly samples the sequence landscape while preserving dinucleotide frequency and the encoded amino acid sequence.
• Artificial sequence generation: Generates artificial sequences that serve as null models for structural comparisons.
• Z-score estimation with structural metrics: Estimates Z-scores using classical structural metrics including the sum of base pairing probabilities and base pairing entropy.
• Structured/unstructured region prediction: Uses structural metrics and Z-scores to predict structured and unstructured regions in input mRNA sequences.

Scientific Applications:

• Identification of functional elements: Identifies candidate functional elements encoded by RNA secondary structures in coding regions that may influence splicing, localization, and translation.
• Study of specific genes: Applied to ASH1 genes to identify key structural elements within their coding regions.

Methodology:

Uniform sampling of sequence space preserving dinucleotide frequency and encoded amino acid sequence, generation of artificial sequences, computation of structural metrics (sum of base pairing probabilities and base pairing entropy), and estimation of Z-scores to predict structured and unstructured regions.