ProkFunFind TutorialΒΆ
This tutorial will walk you through how to use the ProkFunFind tool to search for putative functions within microbial genomes. This tutorial will cover the query format used by ProkFunFind, how to generate the annotation files, and how to perform searches using ProkFunFind. The tutorial has been designed so that each section can be run independently of the others. Each section will also include pre-generated input and output files for you to look at while going through the tutorial.
The tutorial materials are available on Github here: PFF Tutorial
These materials can be downloaded using the following command:
git clone https://github.com/nlm-irp-jianglab/ProkFunFind.git
All tutorial steps can be run from within the root directory of the repository. From this root directory you should see the following files and directories:
File/Directory |
Content |
|---|---|
genomes/ |
Directory containing genomes to search during the tutorial |
queries/ |
Directory containing query input files organized in subdirectories |
precomputed-out/ |
Directory containing precomputed output from each tutorial step |
out/ |
Directory where tutorial output will be generated |
ebi-list.tsv |
Search genome table for EBI genome tutorial |
genome-list.tsv |
Search genome table for main tutorial materials |
A complete set of precomputed output from each step in the tutorial is included in the precomputed-out/ directory. This directory mirrors what would be generated during the tutorial in the out/ directory.
For instructions on how to install ProkFunFind please see: Installation