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Sharing and archiving nucleic acid structure mapping data

By Philippe Rocca-Serra, Stanislav Bellaousov, Amanda Birmingham, Chunxia Chen, Pablo Cordero, Rhiju Das, Lauren Davis-Neulander, Caia D.S. Duncan, Matthew Halvorsen, Rob Knight, Neocles B. Leontis, David H. Mathews, Justin Ritz, Jesse Stombaugh, Kevin M. Weeks, Craig L. Zirbel and Alain Laederach

Abstract

Nucleic acids are particularly amenable to structural characterization using chemical and enzymatic probes. Each individual structure mapping experiment reveals specific information about the structure and/or dynamics of the nucleic acid. Currently, there is no simple approach for making these data publically available in a standardized format. We therefore developed a standard for reporting the results of single nucleotide resolution nucleic acid structure mapping experiments, or SNRNASMs. We propose a schema for sharing nucleic acid chemical probing data that uses generic public servers for storing, retrieving, and searching the data. We have also developed a consistent nomenclature (ontology) within the Ontology of Biomedical Investigations (OBI), which provides unique identifiers (termed persistent URLs, or PURLs) for classifying the data. Links to standardized data sets shared using our proposed format along with a tutorial and links to templates can be found at http://snrnasm.bio.unc.edu

Topics: Bioinformatics
Publisher: Cold Spring Harbor Laboratory Press
OAI identifier: oai:pubmedcentral.nih.gov:3138558
Provided by: PubMed Central
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