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I used that xsd to create the original Java classes and it was out of sync with the classes so I removed it from the tree. Once things settle a bit we'll look into writing a correct xsd.
That said, you're right that the classes should restrict the sequence string so I'll leave this open.
The datatype for the DNA sequence string needs to be a custom restriction on xsd:string that restricts characters to those that are legal for IUPAC.
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