Mercator has moved to www.plabipd.de
Given the increased demand for Mercator, we have moved it to a new faster infrastructure on www.plabipd.de/portal. This will support a greater number of concurrent jobs and will reduce the queueing time.
The results produces are identical but users can now submit larger jobs (this may be increased further pending a further upgrade).
Mercator is a tool to batch classify protein or gene sequences into MapMan functional plant categories. Many MapMan categories deal with metabolic pathways and enzyme functions, therefore using this pipeline a draft metabolic network can be established, especially after manual corretion of the automatically derived classification see e.g. May et al. 2008.
The results of the individual searches are then weighted by reliability. E.g. Uniref gets a low reliability since all proteins from Uniref90 are only classified based on keywords. The classifications with the highest reliabilty are retained. Current statistics (December 08):
To start a MapMan cluster job click "Create New Job".
Step 1 Sequence upload and option setup
You will be presented with an interface asking you for:
Step 2 Check if everything is ok
Press "update job" to check if your submission is ok. You will get a small summary of your submission, in this case 22 sequences comprising 11361 nucleotides were submitted. If everything went ok, you will be presented with a new link: start Mercator
You will then be presented with a web site showing your sequence options, and the current status of your job.
Step 3 Completion of batch job and download
Upon completion you will be offered a download link.
The file is available in zip format. After unziping the file you can open it in MapMan, in a text editor, or in MS Excel. If you open the file using excel, make sure that excel keeps everything formatted as text. (There are bins like 26.10 which get rounded or interpreted as dates by Excel sometimes)
May, P., Wienkoop, S., Kempa, S., Usadel, B., Christian, N., Rupprecht, J., Weiss, J., Recuenco-Munoz, L., Ebenhöh, O., Weckwerth, W., Walther, D (2008) Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii. Genetics. 179:157-66.
Howell, K.A., Narsai, R., Carroll, A., Ivanova, A., Lohse, M., Usadel, B., Millar, A.H., Whelan, J. (200X) Mapping metabolic and transcript temporal switches during germination in Oryza sativa highlights specific transcription factors and the role of RNA instability in the germination process. Plant Physiol. accepted
Crowhurst, R.N., et al. (2008) Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening. BMC Genomics. 9:351.