Mercator

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.
For a sequence clasification Mercator performs:

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):

  • Accuracy ca. 90%
  • Domains and families > 1000
  • Proteins and genes > 30.000

You might also want to try out our new service for MapMan X4. This is much faster (>10x) and shows a higher granularity and precision of BINS but doesn't cover quite as many gene models yet, and requires updated pathway files from within MapMan.

Please evaluate this service! Give your feedback

Start Mercator Job

General
Parameters
TAIR:   TAIR Release 10
PPAP:   SwissProt/UniProt Plant Proteins
CHLAMY:   JGI Chlamy release 4 Augustus models
ORYZA:   TIGR5 rice proteins
KOG:   Clusters of orthologous eucaryotic genes database (KOG)
CDD:   Use conserved domain database
IPR:   Include interpro scan (long runtime)
BLAST_CUTOFF: 
MULTIPLE:   Allow multiple bin assignments
CONSERVATIVE:   Consider the "unassigned" bin with equal weight when assigning bincodes.
ANNOTATE:   Append database annotation to mapping
IS_DNA:   Sequence file contains DNA sequence
Input Sequence

PLEASE NOTE:
Maximally 30 * 106 symbols (nucleotides or aminoacids) may be uploaded in FASTA format.
If you would like to submit a larger data set, please contact us.