Filling gaps with refineGEMs

Warning

Will be deprecated from version 2.0.0 onwards.
New options for gap filling can be found under refinegems.classes.gapfill.

There are two possibilities to use refineGEMs to fill gaps.

Manual gap filling

Automated gap filling

The gapfill module was created to enable an automatic way of filling gaps in a model via genes.

Warning

Current restrictions:

  • Only bacteria supported as missing reactions are filtered by compartments (‘c’, ‘e’, ‘p’).

  • Only models where the organisms have entries in KEGG and/or BioCyc can be gap filled.

Run times:

  • ‘KEGG’: ~ 1h 10mins

  • ‘BioCyc’: ~ 10mins

  • ‘KEGG+BioCyc’: ~ 1h 20mins

The module gapfill can be used to:

a. perform gap analysis

b. add genes, metabolites and reactions from an Excel table to a model

c. or perform gap analysis and add the result directly to a model.

Warning

To use the gap analysis and directly add the result to a model, currently, one of the options ‘BioCyc’ or ‘KEGG+BioCyc’ has to be selected. For all other options the usage of gap_analysis combined with gapfill_model will result in an error.

Relevant parameters

To perform the gap analysis the following parameters are relevant for the config.yaml file: (See Data acquisition from BioCyc on how to obtain the files 1 to 3)

gap_analysis: TRUE
    gap_analysis_params:
      db_to_compare: 'One of the choices KEGG|BioCyc|KEGG+BioCyc'
      organismid: 'KEGG Organism ID' # Needs to be specified for KEGG
      gff_file: 'Path to RefSeq GFF file' # Needs to be specified for KEGG
      biocyc_files:
        - 'File 1: Path to gene to reaction mapping table'
        - 'File 2: Path to reaction table'
        - 'File 3: Path to compounds table'
        - 'File 4: Path to protein FASTA file used as input for CarveMe'

To add genes, metabolites and reactions from an Excel table to a model the following parameters need to be set: (The Excel file is either obtained by running gapfill_analysis or created by hand with the same structure as the result file from gapfill_analysis. An example Excel file to fill in by hand can be found in the cloned repository under data/modelName_gapfill_analysis_date_example.xlsx)

gapfill_model: TRUE
    gap_analysis_file: 'Path to Excel file with which gaps in model should be filled'

Data acquisition from BioCyc

  1. If you have no BioCyc account you will need to create one. See BioCyc /> Create Free Account <https://biocyc.org/new-account.shtml> to create an account.

  2. Then you need to search for the strain of your organism.

  3. Within the database of your organism you need to click on Tools in the menu bar and select Special SmartTables under SmartTables. There you need to make an adjustable copy of each of the tables “All genes of <organism>” and “All reactions of <organism>”.

  4. For the gene to reaction mapping table:

    1. Remove all columns except ‘Gene Name’ from the “All genes of <organism>” table,

    2. then click choose a transform and select ‘Reactions of gene’,

    3. then add the property ‘Accession-2’

    4. and delete the ‘Gene Name’ column.

    5. After that select the column ‘Accession-2’ and use the filter function in the box on the right side of the page to delete all empty rows.

    6. Finally, click Export to Spreadsheet File from the box on the right side and choose Frame IDs.

  5. For the reactions table:

    1. Remove all columns except ‘Reaction’ from the “All reactions of <organism>” table,

    2. then click choose a transform:

      1. select ‘Reactants of reaction’,

      2. then select ‘Products of reaction’

    3. and then choose the property:

    1. ‘EC-Number’,

    2. then ‘Reaction-Direction’,

    3. and then ‘Spontaneous?’.

    1. Finally, click Export to Spreadsheet File in the box on the right side and choose Frame IDs.

  6. For the metabolites table:

    1. Use the MetaCyc database to get the table “All compounds of MetaCyc”.

    2. Remove all columns except ‘Compound’,

    3. then choose the property:

    1. ‘Object ID’,

    2. then ‘Chemical Formula’,

    3. then ‘InChI-Key’,

    4. and then ‘database links’ > ‘ChEBI’.

    1. Finally, click Export to Spreadsheet File in the box on the right side and choose common names.