Predicting biosynthetic gene clusters in genomes
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README.md

ClusterFinder

Predicting biosynthetic gene clusters in genomes. Authors: Peter Cimermancic & Michael Fischbach

Requirements:

  • python (2.X)
  • numpy

Instructions:

  • an example of input file: example_input.txt: COLUMN DESCRIPTION:

    1. GeneID
    2. Sequencing status
    3. Organism name
    4. Scaffold OID
    5. Organism OID
    6. Locus Tag
    7. Gene Start
    8. Gene End
    9. Strand
    10. Pfam Template Start
    11. Pfam Template End
    12. Pfam Start
    13. Pfam End
    14. PfamID
    15. Pfam E-score
    16. Enzyme ID
  • if your input file format differs from the one above, please modify the file or lines 51-55 of the ClusterFinder.py script

  • an example of running ClusterFinder is shown in ClusterFinder.py script DESCRIPTION:

    1. modify paths (if not running from ClusterFinder directory - lines 7, 19 & 20)
    2. name the organism and the input file - lines 15 & 16
    3. run: python ClusterFinder.py
  • testing run: python ClusterFinder.py without making any changes to the files

  • OUTPUT1 [organims_name.out]: same as input + a column with probability values

  • OUTPUT2 [organism_name.clusters.out]: same as OUTPUT1, but only for the domains from gene clusters that have passed the filtering steps.