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Permits the description of higher level information about the data including, but not restricted to, base pairs, base triples, and pseudoknots. RNAML is a syntax that allows storage and exchange of information about RNA sequence and secondary and tertiary structures. The RNAML syntax has been designed with two purposes in mind: (i) a syntax that is both immediately adoptable by application builders in RNA science and capable of allowing one to represent a large amount of application-independent information in an unambiguous and reusable syntax, and (ii) a syntax that can easily be expanded as new types of information become available.

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RNAML versioning

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RNAML classification

RNAML specifications

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Command line interface
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RNAML support


  • François Major <>


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Stanford Medical Informatics, Stanford University Medical Center, Stanford, CA, USA; Département d’Informatique et de Recherche Opérationnelle, Université de Montréal, Montréal, QC, Canada; Department of Microbiology, North Carolina State University, Raleigh, NC, USA; Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA; Centre National de la Recherche Scientifique, Marseille, France; Department of Biochemistry, University of Alabama at Birmingham, Birmingham, AL, USA; Department of Chemistry, Bowling Green State University, Bowling Green, OH, USA; Department of Chemistry, Rutgers University, Piscataway, NJ, USA; IBMC-Centre National de la Recherche Scientifique, Strasbourg, France; Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA

Funding source(s)

This work was supported by National Institutes of Health Grant LM06244, National Science Foundation Grant DBI-9600637 and the Canadian Institutes of Health Research.

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