RNAStructAlignmentML

From BioSchemas

RNAStructAlignmentML is a format for storing RNA secondary structure alignments as computed by e.g. RNAforester or RNAalifold . RNAStructAlignmentML uses an RNAStructML-like architecture, but bases on AlignmentML instead of SequenceML.

1 Example
- 1.1 FASTA DotBracket Format
- 1.2 RNAStructAlignmentML Format
2 History
3 Author

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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)]
   UCACCCCUCUC-UGC-CUU---U-UGGAGAGUUGGUCAGC-UC-UCAGCUGACCUUAGGGGUGGAUCUGGCUUUCCCAA-
   U-U-GGUUUACUCCGA-UUGGGUUGGCUGAAGCUUAGAGGCUUAAGCAAGGACCCGAUAUGGGCUUCAACUGGAUAGGUA
   GCACCGGCUCCUGCCGACUACACGAAGUUGUGGCUUGUGGACUUUGCUAGAGGCCAAGCAG-GA-A-A-CAUGCUUUGCA
   UGUUUU-AAACUUU
   (((((((((((-(.(-(..---.-.))))))..(((((((-..-...)))))))..)))))))).((.((((..(((((-
   (-(-((......))))-)))))..)))))).((((...(((((.(((((((.((....(..((((.(((((......(((
   (...((((....)))).))))....))))).))))..))).)))))))..)))))))))..-((-(-(-(((((...)))
   ))))))-.......
   >gi|37727738|gb|AY170854.1| Scenedesmus arcuatus var. arcuatus [Scenedesmus arcuatus var. arcuatus (modified and secondary structure added)]
   UCACCCCUC---C-CACCU-----UGU-GGGUCGGUUGGCUUG-CUAGCUAGCCUUAGGGGUGGAUCUGGCUUCCCCAA-
   U-UUGCUUU--UGUGGAUUGGGUUGGCUGAAGUGUAGAGGCUUAAACAAGGACCCGAUAUGGGCUUCAACUGGAUAGGUA
   GCACCGGCUC-UGCCGACUACACGAAGUUGUGGCCUGUGGACCUUGUUAGAGGCCAAGCAG-GA-A-A-CAUGCUUGGCA
   UGU-UUUAAACUUU
   (((((((((---(-(((..-----.))-)))..((((((((..-..))))))))..))))))))....((((..(((((-
   (-(..(...--.)..)))))))..))))....(((...(((((.(((((((.((....(((((((.(((((......(((
   (...((((..-.)))).))))....))))).))))))))).)))))))..)))))..))).-((-(-(-(((((...)))
   )))-))).......

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RNAStructAlignmentML Format

   <?xml version="1.0" encoding="UTF-8"?>
   <rnastructAlignmentML
       xmlns="http://hobit.sourceforge.net/xsds/20060515/rnastructAlignmentML"
       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
       xsi:schemaLocation="http://hobit.sourceforge.net/xsds/20060515/rnastructAlignmentML 
                           http://bibiserv.techfak.uni-bielefeld.de/xsd/net/sourceforge/hobit/20060515/nastructAlignmentML.xsd">
       <rnastructurealignment id="IDDP8YM3vFxV">
           <sequence seqID="gi|4972014|emb|AJ237949.1|SAC237949" size="254">
               <name>Scenedesmus acuminatus</name>
               <description>Scenedesmus acuminatus</description>
               <alignedNucleicAcidSequence>UCACCCCUCUC-UGC-CUU---U-UGGAGAGUUGGUCAGC-UC-UCA....</alignedNucleicAcidSequence>
               <structure>(((((((((((-(.(-(..---.-.))))))..(((((((-..-.......</structure>
               <comment>modified and secondary structure added</comment>
           </sequence>
           <sequence seqID="gi|37727738|gb|AY170854.1|" size="254">
               <name>Scenedesmus arcuatus var. arcuatus</name>
               <description>Scenedesmus arcuatus var. arcuatus</description>
               <alignedNucleicAcidSequence>UCACCCCUC---C-CACCU-----UGU-GGGUCGGUUGGCUUG-CUAG....</alignedNucleicAcidSequence>
               <structure>(((((((((---(-(((..-----.))-)))..((((((((..-..)....</structure>
               <comment>modified and secondary structure added</comment>
           </sequence>
       </rnastructurealignment>
   </rnastructAlignmentML>

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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