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Comparative genomics : Pan-phylum Comparison of Nematode Metabolic Potential

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[Sept.15.2015]   
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Pan-phylum Comparison of Nematode Metabolic Potential

Images showing module structures and KO presence for each species separately. Note that for non-linear modules, these figures may be misleading. For these, the current module structure image on KEGG website is likely to be helpful.

Select a species and module from the tables below and click Submit. You will be taken to the module structure for that specific combination. Note that you must select one choice from each list, otherwise this same page will re-load.

Species selectionModule selection

Software

The program used to determine module completeness is available for download here:

modDFS.tar.bz2  (md5sum: e7b3012b7618206fc4ed516339c32544)

Users provide the following information:

1. Available KOs in the dataset, module's definition, and reaction data in input files.
2. Whether the module is (even partially) cyclic (default is assumed to be acyclic, and the results for such modules need to be manually checked).
3. Any "given compounds" in the module. i.e. compounds that are available to the module from external sources. these are generally the substrates of the first reaction step of an acyclic module (this is assumed to be the default), but do not necessarily exclude other compounds. For instance, there might be other reactions whose substrates aren't produced by any reaction in the module. these subsrates need to be pointed out by the user.

The script will output information on module completeness. A README is included in the package with full instructions.


 
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