skip to navigation
skip to content

shogen 1.4.3

Finding shortest genome segments that regulate metabolic pathways.


You can install shogen by running:

$ pip install --user shogen

On Linux the executable script can then be found in ~/.local/bin

and on MacOS the script is under /Users/YOURUSERNAME/Library/Python/2.7/bin.


Typical usage is:

$ [options] genomefile metabolismfile catalysationfile queries

  -h, --help   show this help message and exit
  -k K, --k=K  Number of ranked  shortest genome segments (Default to 5)
  -l L, --l=L  maximum length of a genome segment (Default to 200)


Sample files for finding functional gene units in e. coli are available here:

genome.txt metabolism.txt catalyze.txt queries.txt

File Type Py Version Uploaded on Size
shogen-1.4.3.tar.gz (md5) Source 2014-11-10 8KB