PARTS -- probabilistic alignment for RNA joinT secondary structure prediction
What you can do:
Joint prediction of alignment and common secondary structures of two RNA sequences.
Highlights:
- The joint consideration of common secondary structures and alignment is accomplished by structural alignment over a search space defined by the newly introduced motif called matched helical regions.
- The matched helical region formulation generalizes previously employed constraints for structural alignment and thereby better accommodates the structural variability within RNA families.
- A probabilistic model based on pseudo free energies obtained from precomputed base pairing and alignment probabilities is utilized for scoring structural alignments.
- Maximum a posteriori (MAP) common secondary structures, sequence alignment and joint posterior probabilities of base pairing are obtained from the model via a dynamic programming algorithm called PARTS.
Keywords:
- Nucleic Acid Conformation
- RNA Sequence Alignment
- RNA Sequence Analysis
- RNA secondary structure
Literature & Tutorials:
This record last updated: 09-02-2008