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mihailefter edited this page May 24, 2019 · 3 revisions

About Mutalyzer

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). Mutalyzer aims to encourage the proper use of nomenclature in publications and reduce redundancy in gene variant databases (LSDBs). In principle, Mutalyzer can check descriptions of sequence variants detected in other organisms, provided that the standard HGVS nomenclature is applied.

Quick overview of Mutalyzer 2 flow.

Help using Mutalyzer 2 functionalities

Name Checker checks complete sequence variant descriptions

Syntax Checker only checks the syntax of the complete sequence variant description

Position Converter converts chromosomal positions to transcript orientated positions and vice versa.

SNP Converter converts a dbSNP rsId to HGVS notation.

Name Generator helps to generate complete sequence variant descriptions

Description Extractor helps to generate the HGVS variant description from a reference sequence and an observed sequence.

Reference File Loader allows you to load and use your own reference sequence.

Batch Checkers are interfaces that accept a list of inputs. These interfaces can be used for large quantities of checks.

Web services provide programmatic access to Mutalyzer 2 functionality via SOAP.

Introduction to

Variant Descriptions

Reference Sequences

Mutalyzer and gene variant databases (including Tips for curators)

Mutalyzer and other organisms

Standard human sequence variant nomenclature in EBNF format

Using Mutalyzer

Mutalyzer Exercise

Citing Mutalyzer

When you use Mutalyzer, please cite this paper: Wildeman M, van Ophuizen E, den Dunnen JT, Taschner PE. Improving sequence variant descriptions in mutation databases and literature using the MUTALYZER sequence variation nomenclature checker. Hum Mutat 29:6-13 (2008)(PMID: 18000842).

Mutalyzer 2 has been completely redesigned by Jeroen F.J. Laros, with help from Martijn Vermaat, Gerben R. Stouten and Gerard C. P. Schaafsma, according to specifications provided by Peter E.M. Taschner and Johan T. den Dunnen. The different parts of the nomenclature checker functionality have been separated into modules, which can be used as independent webservices and undergo further development and extension in the future.

Errors and feature requests

Any error message gives an indication of the problem encountered and replicates the input of the user. Most errors occurring after mistyping should be easy to understand and can be corrected immediately by altering the data in the field specified. In other cases, Mutalyzer should advise you to contact us when the error persists. Please specify your input and which tool you used.

Occasionally, Mutalyzer will display an Internal Server Error message due to unexpected behavior. You can use Mutalyzer's bugtracking system to report errors and send in feature requests.

Mailing lists

The Mutalyzer mailing list is a general discussion list for Mutalyzer. Messages can be posted to this list via the Google Groups interface or by sending an email to

The Mutalyzer Announcements mailing list is a low-volume mailing list for announcing updates to Mutalyzer. Consider subscribing if you are a regular user of the Mutalyzer webservices or are maintaining your own Mutalyzer installation.

Source code

The Mutalyzer source code is Open Source and available under the GNU Affero General Public License (AGPL).

Development of Mutalyzer happens on GitHub. Contributions are very welcome! They can be feature requests, bug reports, bug fixes, unit tests, documentation updates, or anything els you may come up with.

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