Welcome to ProkFunFind’s documentation!

ProkFunFind is a pipeline that can be used to predict genes related to function of interest. Criteria for function detection include presence of detected genes, and genomic co-localization.


In order to identify genes using ProkFunFind, the user needs:

  1. Select the correct search approaches and filtering parameters to identify your genes of interest

    • Protein sequences

    • Profile HMMs

    • COGs

    • KOs

    • Protein domain signatures

  2. Define the gene components for the function system in JSON format

    • Define the essential and non essential components of the overall function of interest.

  3. Perform the search for the functions in your genomes of interest using ProkFunFind

  4. Analyze the search results

  • Assess completeness of function in different organisms

  • Identify potential gene clusters

  • Analyze species distribution