clementmlay / nitrogenasefinder

This is the master repo for Nitrogenase Finder. See the readme or the website for use info!

** A Nitrogenase(Gene) Search Tool and Visualization Maker

*Description:

Nitrogenase Finder is a program that finds percentage similarities between a gene and open reading frames (ORFs) in a genome or metagenome which is comprised of a set of contigous regions ("contigs"). It identifies the similarities using a memoized levenstein distance algorithm. Nitrogenase_finder.py returns a list of dictionaries for each plaustibly-sized ORF that contains the length of the ORF, the start and end locations of the ORF, a flag indicating forward or reverse complement location, and the percentage match between the ORF and the gene, in addition to the length of the gene being used and the levenshtein distance, which are not used in the visualization but are present for debugging reasons in the dictionaries. When the algorithm identifies a match higher than the user-set percent similarity threshold, it visualizes the ORF in varying shades of green; non-matches (determined by having a percent similarity below the threshold) and non-ORF DNA are visualized in black. The locations of these ORFs may be found by mousing over the ORF of interest, which will cause the start and end index (in nucleotides, counting from zero) of the ORF to appear, in addition to the name of the contig on which the ORF is located.

*Authors: Rebecca Gettys, Erica Lee, and Liv Kelley Microbial Metagenome from Dr. Jean Huang

A code snippet used for the recursive levenshtein memoized distance can be found here; it walked us through the implementation and we based ours on this. We also used the code contained in the base repository for the Software Design Miniproject 1 (Gene Finder) which can be found on Github.

*Getting Started and Usage:

Download this program's lastest version from GitHub and install Pygame (and Python 2.7 if you don't already have it!). If you would like to run it using the default nitrogenase sequence and metagenome, simply run nitrogenase_finder.py, followed by visualization.py. If you would like to run this program on metagenomes other than those provided by Jean Huang, edit the load_metagenome function in load.py to point to the appropriate file. If you would like to run this program to look for genes other than nitrogenase, edit the load_nitrogenase function in load.py to point to a file that contains the proper gene sequence. Please note that if the formatting or file structure on either your metagenome or on your nitrogenase is different than what we have, you will need to either change the code to match your data's formatting or change your formatting to match ours.

Requirements: This program runs on python 2.7. It uses the sys and pickle modules, which are built into Python 2. Additionally, it uses PyGame for the visualization component (http://pygame.org/hifi.html), and which you will need to have installed in order to utilize our program.

This program is released as is, with no guarantees to it's function, under the MIT license. Hold the authors harmless and check your outputs for rationality - there be BUGS out there!