AlignmentML

From BioSchemas

AlignmentML is a format describing (multiple) alignment information any alignment program like CLUSTALW, DCA and Dialign can produce. Similar to SequenceML, different sequence types are supported.

1 Example
- 1.1 FASTA Format
- 1.2 AlignmentML Format
2 History
3 Authors

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Example

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FASTA Format

   >gi|58374180|gb|AAW72226.1| HA [Influenza A virus (A/duck/Shandong/093/2004(H5N1))]
   m--eeivlllaivslvksdqicigyhannsteqvdtimeknvtvthaqdilekthngklcdldgvkplilrdcsvagwll
   gnpmcdefinvpewsyivekanpandlcypgdfndyeelkhllsrinhfekiqiipksswsdheassgvssacpyngks-
   sffrnvvwlik-knssyptikrsynntnqedllilwgihhpndaaeqtklyqnpttyisvgtstlnqrlvpkiatrskvn
   gqsgrmeffwtilkpndainfesngnfiapeyayki---vk-kgdsaimkseleygnc-ntkcqtpm-gainssmpfhni
   hpltigecpkyvksnrlvlatglrntpqrerrr-kkrglfgaiagfieggwqgmvdgwygyhhsneqgsgyaadkestqk
   aidgvtnkvnsiidkmntqfeavgrefnnlerrienlnkkmedgfldvwtynaellvlmenertldfhdsnvknlydkvr
   lqlrdnakelgngcfefyhkcdnecmesvkngtydypryseearlnreeisgvklesmgtyqilsiystvasslalaimv
   aglslwmcsngslqcrici-----
   >gi|28849361|gb|AAO52863.1|AF509020_1 hemagglutinin [Influenza A virus (A/Pheasant/Hong Kong/FY155/01 (H5N1))]
   -------------slvksdqicigyhannsteqvdtimeknvtvthaqdilekthngklcdldgvkplilrdcsvagwll
   gnpmcdefinvpewsyivekaspandlcypgdfndyeelkhllsrinhfekiqiipksswsnheassgvssacpylgks-
   sffrnvvwlik-knnayptikrsynntnqedllvlwgihhpndaaeqtklyqnpttyisvgtstlnqrlvpkiatrskvn
   gqsgrmeffwtilkpndainfesngnfiapeyayki---vk-kgdsaimkseleygnc-ntkcqtpm-gainssmpfhni
   hpltigecpkyvksnrlvlatglrntpqrerrr-kkrglfgaiagfieggwqgmvdgwygyhhsneqgsgyaadkestqk
   aidgvtnkvnsiidkmntqfeavgrefnnlerrienlnkkmedgfldvwtynaellvlmenertldfhdsnvknlydkvr
   lqlrdnakelgngcfefyhkcdnecmesvkngtydypqylrkaglnreeisgvklesmgtyqilsiystvasslalaimv
   aglslwmcsngslqcrici-----
   >gi|108671045|gb|ABF93441.1| hemagglutinin [Influenza A virus (St Jude H5N1 influenza seed virus 163222)]
   m--ekivlllaivslvksdqicigyhannsteqvdtimeknvtvthaqdilekthngklcdldgvkplilrdcsvagwll
   gnpmcdeflnvpewsyivekinpandlcypgnfndyeelkhllsrinhfekiqiipksswsdheassgvssacpyqgrs-
   sffrnvvwlik-knnayptikrsynntnqedllvlwgihhpndaaeqtrlyqnpttyisvgtstlnqrlvpkiatrskvn
   gqsgrmeffwtilkpndainfesngnfiapenayki---vk-kgdstimkseleygnc-ntkcqtpi-gainssmpfhni
   hpltigecpkyvksnrlvlatglrnspqie-----trglfgaiagfieggwqgmvdgwygyhhsneqgsgyaadkestqk
   aidgvtnkvnsiidkmntqfeavgrefnnlerrienlnkkmedgfldvwtynaellvlmenertldfhdsnvknlydkvr
   lqlrdnakelgngcfefyhrcdnecmesvrngtydypqyseearlkreeisgvklesigtyqilsiystvasslalaimv
   aglslwmcsngslqcrici-----

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AlignmentML Format

   <?xml version="1.0" encoding="utf-8"?>
   <alignmentML 
       xmlns="http://hobit.sourceforge.net/xsds/20060602/alignmentML" 
       xmlns:NS1="http://www.w3.org/2001/XMLSchema-instance" 
       NS1:schemaLocation="http://hobit.sourceforge.net/xsds/20060602/alignmentML 
                           http://bibiserv.techfak.uni-bielefeld.de/xsd/net/sourceforge/hobit/20060602/alignmentML.xsd">
       <alignment>
           <sequence seqID="gi|58374180|gb|AAW72226.1|">
               <name>HA</name>
               <description>Influenza A virus (A/duck/Shandong/093/2004(H5N1))</description>
               <alignedAminoAcidSequence>M--EEIVLLLAIVSLVKSDQICIGYHANNSTEQVDTIMEK....</alignedAminoAcidSequence>
           </sequence>
           <sequence seqID="gi|28849361|gb|AAO52863.1|AF509020_1">
               <name>hemagglutinin</name>
               <description>Influenza A virus (A/Pheasant/Hong Kong/FY155/01 (H5N1))</description>
               <alignedAminoAcidSequence>-------------SLVKSDQICIGYHANNSTEQVDTIMEK....</alignedAminoAcidSequence>
           </sequence>
           <sequence seqID="gi|108671045|gb|ABF93441.1|">
               <name>hemagglutinin</name>
               <description>Influenza A virus (St Jude H5N1 influenza seed virus 163222)</description>
               <alignedAminoAcidSequence>M--EKIVLLLAIVSLVKSDQICIGYHANNSTEQVDTIMEK....</alignedAminoAcidSequence>
           </sequence>
       </alignment>
   </alignmentML>

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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