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Hum Mutat. 2016 Apr;37(4):344-9. doi: 10.1002/humu.22954. Epub 2016 Feb 4.

VariOtator, a Software Tool for Variation Annotation with the Variation Ontology.

Author information

1
Protein Structure and Bioinformatics, Department of Experimental Medical Science, Lund University, BMC B13, Lund, SE-221 84, Sweden.

Abstract

The Variation Ontology (VariO) is used for describing and annotating types, effects, consequences, and mechanisms of variations. To facilitate easy and consistent annotations, the online application VariOtator was developed. For variation type annotations, VariOtator is fully automated, accepting variant descriptions in Human Genome Variation Society (HGVS) format, and generating VariO terms, either with or without full lineage, that is, all parent terms. When a coding DNA variant description with a reference sequence is provided, VariOtator checks the description first with Mutalyzer and then generates the predicted RNA and protein descriptions with their respective VariO annotations. For the other sublevels, function, structure, and property, annotations cannot be automated, and VariOtator generates annotation based on provided details. For VariO terms relating to structure and property, one can use attribute terms as modifiers and evidence code terms for annotating experimental evidence. There is an online batch version, and stand-alone batch versions to be used with a Leiden Open Variation Database (LOVD) download file. A SOAP Web service allows client programs to access VariOtator programmatically. Thus, systematic variation effect and type annotations can be efficiently generated to allow easy use and integration of variations and their consequences.

KEYWORDS:

LOVD; LSDB; Variation Ontology; annotation; bioinformatics; database; mutation; ontology; software; variation

PMID:
26773573
DOI:
10.1002/humu.22954
[Indexed for MEDLINE]

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