title: RNAdigest: a web-based tool for the analysis and prediction of structure-specific RNAse digestion results.
abstract: Despite recent developments in analyzing RNA secondary structures, relatively few RNA structures have been determined. To date, many investigators have relied on the traditional method of using structure-specific RNAse enzymes to probe RNA secondary structures. However, if these data were combined with novel computational approaches, investigators would have an informative and valuable tool for RNA structural analysis. To this end, we created the web server "RNAdigest." RNAdigest uses mfold RNA structural models in order to predict the results of RNAse digestion experiments. Furthermore, RNAdigest also utilizes both RNA sequence and the experimental digestion patterns to formulate the constraints for predicting secondary structures of the RNA. Thus, RNAdigest allows for the structural interpretation of RNAse digestion experiments. Overall, RNAdigest simplifies RNAse digestion result analyses while allowing for the identification of unique fragments. These unique fragments can then be used for testing predicted mfold structures and for designing structural-specific DNA/RNA probes.
authors.affiliation: Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland.
authors.forename: Piotr
authors.initials: P
authors.lastname: Madanecki
authors.affiliation: Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America.
authors.forename: Susan
authors.initials: S
authors.lastname: Nozell
authors.affiliation: Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland.
authors.forename: Renata
authors.initials: R
authors.lastname: Ochocka
authors.affiliation: Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America.
authors.forename: James F
authors.initials: JF
authors.lastname: Collawn
authors.affiliation: Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland.
authors.forename: Rafal
authors.initials: R
authors.lastname: Bartoszewski
mesh_terms: D020407:Internet; D009690:Nucleic Acid Conformation; D012313:RNA / Q000032:analysis / Q000737:chemistry*; D014584:User-Computer Interface
chemical_list: D012313:RNA