Adding a new organism to Mutalyzer

Introduction

In this document, we describe what is needed for Mutalyzer to support new organisms. For each functionality, we give a list of requirements and an estimate of the amount of time needed for implementation.

Position converter

To use the position converter, we need a mapping database for the genomic reference sequence that is used. The database should contain the following information per gene:

• Genomic location (chromosome, transcription start, transcription end).
• Gene model (CDS start, CDS stop, all splice sites).

The transcription start and end may be missing, but this is not recommended.

Implementation time

Depending on the format of the database, making this functionality available is relatively straightforward. If the database is stored in a structured format (CSV or something that can be converted to CSV automatically), importing should take no more than two working days.

Name checker

To use the name checker, a fully annotated GenBank record should be available for every genomic location.

Public genome build

If the genome build of the organism in question is public, as is the case for some model organisms, the GenBank records can be retrieved from the NCBI. In this case, no special effort is required.

If the data is public, but is not yet available as a genome build at the NCBI, the mapping database can be converted to the format required by the NCBI and uploaded. The conversion should take no more than two working days, but the time it will take before the build is available depends on the NCBI.

Non public genome build

If it is not possible to submit the generated GenBank reference files to the NCBI, for commercial reasons for example, there is the option to offer a stand-alone version of Mutalyzer containing the reference files. This version should be hosted at the client side. Preparing such an installation will require no more than three working days.

Additional notes

There is currently no program available for the generation of the GenBank reference files. Although this is a one time effort, we estimate that the development of such a program requires three weeks.

There is also no program available for the conversion of a mapping database to the format the NCBI expects. The specifications are also unknown. Once we have the specifications, we estimate that the development of a conversion tool will take three weeks.

A stand-alone version of Mutalyzer will require some expertise to set up and maintain at the client side. Although we currently provide no support or maintenance, we are thinking about a model for this.