Mutalyzer

Mutalyzer was primarily developed to check the description of sequence variants identified in a gene during genetic testing according to the rules of the standard human sequence variant nomenclature of the Human Genome Variation Society. The Mutalyzer 2 parser is based on a formalized description of the nomenclature in Extended Backus-Naur Form. Mutalyzer applies the nomenclature rules and corrects variant descriptions accordingly.

This content is being maintained by P.Taschner.

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Documentation

See Mutalyzer help and Mutalyzer Feedbackfor detailed documentation.

Mutalyzer is a tool primarily designed to check descriptions of sequence variants according to the standard human sequence variant nomenclature of the Human Genome Sequence Variation Society (HGVS) (For an overview, visit http://www.hgvs.org/mutnomen/). Mutalyzer aims to encourage the proper use of nomenclature in publications and reduce redundancy in sequence variation databases. In principle, Mutalyzer can check descriptions of sequence variants detected in other organisms, provided that the standard HGVS nomenclature is applied.

Mutalyzer 2 flow
The user specifies a reference sequence (file) and a variant using the Name Generator or the Name checker interface. The Name Generator builds the complete variant description for the Name Checker (e.g., Mutalyzer uses this input to perform the nomenclature check in the following steps:

1) Retriever: retrieves reference sequence records from the NCBI or LRG websites.

2) Reference sequence parser: extracts sequence and annotation from reference sequence records

3) Syntax checker: context-free parser using the complete sequence variant description to check whether the syntax is correct according to standard HGVS sequence variant nomenclature

4) Name checker: the core nomenclature checker using the complete sequence variant description to check whether it is correct according to standard HGVS sequence variant nomenclature

Additional Mutalyzer 2 functionality:

- Position Converter: converts hg18 and hg19 chromosomal positions to transcript positions in HGVS n. or c. notation and vice versa. The n. or c. notation should be checked with the Name checker.

- GenBank Uploader: allows you to upload and use your own reference sequence.

- SNP converter: allows you to convert a dbSNP rsId to HGVS notation.

- Batch Checkers: interfaces for the different checkers that accept a large list of descriptions as input.

- Web services: programmatic access to Mutalyzer's functionality.