Mercator - a plant protein annotation tool

Mercator4 is an online tool to assign functional annotations to land plant protein sequences. The functional annotation includes the biological context of a protein and ends with the description of the function of the protein (e.g. Photosynthesis.photorespiration.phosphoglycolate phosphatase). The Mercator4 annotation is retrieved from Mapman4, a framework that arranges all available plant protein categories (called BINs) embedded in a hierarchical structure of context descriptions. Learn more about the Mapman4 framework in a recent publication (Schwacke et al. 2019). The current version of Mercator4/Mapman4 is v.3 (August 2020).

Mercator v.3.6 is an older version of Mercator based on an older version of the Mapman framework (Lohse et al. 2014). The Mercator v.3.6 online tool is still available but active maintenance has ended.

How to use the Mercator4 annotation tool

Launch the Mercator4 website and enter your plant protein sequences in a valid FASTA format. It is also possible to submit nucleotide sequences (specify sequence type 'DNA') which will be internally translated into protein sequences. Beforehand, the validity of the FASTA format can be tested by the Mercator FASTA validator.
After submitting the sequences, the Mercator4 website keeps you informed about the status of your job. In general, the functional annotation of a couple of thousands of plant protein sequences takes only a few minutes.

Mercator4 annotation data online

When the job has been finished, you can download the results for further processing on your local computer (click on 'Mercator4 annotation results'). In addition, the results can be displayed online.

Mapman desktop application

The Mapman desktop application displays the Mercator annotation results combined with gene expression data onto diagrams of metabolic pathways or other processes. This requires an installation of the Mapman desktop application (available for MS Windows, MacOS and Linux) on your local computer.

For the display, you will need a pathway diagram, the Mercator annotation results and gene expression data. Notice, that protein/gene identifiers have to be identical (case sensitive) in both the Mercator annotation file and the gene expression file (see examples below).

Diagrams for the Mapman desktop application

The Mapman desktop application requires a diagram that illustrates the pathway or process to be visualized. Each diagram consists of a pathway image file (.svg) and an extra protein/gene mapping file (.xml). Notice, the diagrams designed for Mercator4 (X4 ..) are not compatible to Mercator v.3.6 and vice versa.

© 2021 Usadel lab, IBG-4, Forschungszentrum Jülich / Heinrich Heine University Düsseldorf