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 latest version is the Mercator4 v.2 online tool (July 2019).
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. 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.
- a bar chart overviews the resulting protein annotations distributed across the 28 available top level context descriptions. Each bar represents a top level context description and the percentage of its protein categories occupied by the submitted protein sequences.
- the Mercator Tree Viewer (click on the tab 'Mercator Tree Viewer') shows details of the protein categorization. Load the results of your job into the tree structure and - optionally - add pre-evaluated protein annotations from one or more of the listed plant species. If you expand the tree diagram at a location of your interest it tells you the protein count per species per category. A mouse-over on a count tab pops up the individual names of the categorized proteins.
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 installation of the Mapman desktop application (available for MS Windows, MacOS and Linux) on your local computer.
- download the Mercator protein annotation result file of your sequences
- on your local computer, provide a gene expression count table file of your sequences (e.g. generated by RobiNA or other tools)
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.
- Mercator4 annotation: download a diagram from the list below and unzip it (the .zip file contains both the pathway image file + the protein mapping file). The list contains the currently available diagrams for Mercator4 and will be extended.
- Mercator v.3.6 annotation: download pathway image files and protein mapping files from the Mapman download site
- alternatively, create an individual pathway diagram for your data. Use your favorite image software to create the background image file and generate the extra protein mapping file within the Mapman desktop application.