RNAStructML

From BioSchemas

RNAStructML is a format for storing RNA secondary structure information. The most widely used application for RNA tools, such as RNAshapes, RNAfold and Mfold is the proprosal of RNA secondary structures, based on thermodynamic principles. RNAStructML is inspired by SequenceML and uses Vienna style DotBracket strings for storing the information about RNA secondary structure.

1 Example
- 1.1 FASTA DotBracket Format
- 1.2 RNAStructML Format
2 History
3 Authors

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Example

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FASTA DotBracket Format

   >gi|4972014|emb|AJ237949.1|SAC237949 Scenedesmus acuminatus [Scenedesmus acuminatus (modified and secondary structure added)]
   UCACCCCUCUCUGCCUUUUGGAGAGUUGGUCAGCUCUCAGCUGACCUUAGGGGUGGAUCUGGCUUUCCCAAUUGGUUUAC
   UCCGAUUGGGUUGGCUGAAGCUUAGAGGCUUAAGCAAGGACCCGAUAUGGGCUUCAACUGGAUAGGUAGCACCGGCUCCU
   GCCGACUACACGAAGUUGUGGCUUGUGGACUUUGCUAGAGGCCAAGCAGGAAACAUGCUUUGCAUGUUUUAAACUUU
   ((((((((((((.((....))))))..(((((((.....)))))))..)))))))).((.((((..(((((((((.....
   .)))))))))..)))))).((((...(((((.(((((((.((....(..((((.(((((......((((...((((....
   )))).))))....))))).))))..))).)))))))..)))))))))..(((((((((...))))))))).......
   >gi|37727738|gb|AY170854.1| Scenedesmus arcuatus var. arcuatus [Scenedesmus arcuatus var. arcuatus (modified and secondary structure added)]
   UCACCCCUCCCACCUUGUGGGUCGGUUGGCUUGCUAGCUAGCCUUAGGGGUGGAUCUGGCUUCCCCAAUUUGCUUUUGUG
   GAUUGGGUUGGCUGAAGUGUAGAGGCUUAAACAAGGACCCGAUAUGGGCUUCAACUGGAUAGGUAGCACCGGCUCUGCCG
   ACUACACGAAGUUGUGGCCUGUGGACCUUGUUAGAGGCCAAGCAGGAAACAUGCUUGGCAUGUUUUAAACUUU
   (((((((((((((...)))))..((((((((....))))))))..))))))))....((((..(((((((..(....)..
   )))))))..))))....(((...(((((.(((((((.((....(((((((.(((((......((((...((((...))))
   .))))....))))).))))))))).)))))))..)))))..))).(((((((((...))))))))).......

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RNAStructML Format

   <?xml version="1.0" encoding="utf-8"?>
   <rnastructML 
       xmlns="http://hobit.sourceforge.net/xsds/20060201/rnastructML" 
       xmlns:NS1="http://www.w3.org/2001/XMLSchema-instance" 
       NS1:schemaLocation="http://hobit.sourceforge.net/xsds/20060201/rnastructML
                           http://bibiserv.techfak.uni-bielefeld.de/xsd/net/sourceforge/hobit/20060201/rnastructML.xsd">
       <rnastructure id="IDc4nOsqjgLG">
           <sequence seqID="gi|4972014|emb|AJ237949.1|SAC237949">
               <name>Scenedesmus acuminatus</name>
               <description>Scenedesmus acuminatus</description>
               <nucleicAcidSequence>UCACCCCUCUCUGCCUUUUGGAGAGUUGGUCAGCUCUCAGCUGACCUUAGGGGUGG....</nucleicAcidSequence>
               <comment>modified and secondary structure added</comment>
           </sequence>
           <structure>((((((((((((.((....))))))..(((((((.....)))))))..)))))))).((.((((..((((....</structure>
       </rnastructure>
       <rnastructure id="IDMkBuPLmLAj">
           <sequence seqID="gi|37727738|gb|AY170854.1|">
               <name>Scenedesmus arcuatus var. arcuatus</name>
               <description>Scenedesmus arcuatus var. arcuatus</description>
               <nucleicAcidSequence>UCACCCCUCCCACCUUGUGGGUCGGUUGGCUUGCUAGCUAGCCUUAGGGGUGGAUC....</nucleicAcidSequence>
               <comment>modified and secondary structure added</comment>
           </sequence>
           <structure>(((((((((((((...)))))..((((((((....))))))))..))))))))....((((..(((((((....</structure>
       </rnastructure>
   </rnastructML>

ATTENTION: To get a better overview of the XML structure, the sequence data is not complete in the shown XML example. Download the complete example here.

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