NifFINDER Files

Federal of Paraná University (UFPR) - Curitiba, Brazil.
Laboratory of Artificial Intelligence Applied to Bioinformatics (AIBIA), Professional and Technical Education Sector - SEPT. 
by Nichio, B T L

Description:
Tool developed in MATLAB to identify the set of proteins encoded by the nifs genes (which they are called Nifs). 
NifFinder identifies up to 24 Nifs plus monC - For each Nif protein an Artificial Neural Network (ANN) was built using SWeeP vectors.

Requisites and observations:
- The Matlab Compiler Runtime (MCR) ver 8.0  is necessary! its freely available at: https://www.mathworks.com/products/compiler/matlab-runtime.html
- The Rbase.mat (~700Mb) is necessary and separated downloadable at: https://mega.nz/file/FglEmJxR#3CV0ALSEVOAXtkTxBqRdW69H8q0Ej0f2EG-c3a7IAzk
- Make you sure you have all the necessary data (NifFinder.exe, RNAnif.mat, Rbase.mat and the protein FASTA or FASTAs)
- The FASTA extension: the algoritm reads all the extensions with the sufix ".f*" (i.e.: ".fa", ".faa", ".fasta")

Usage: 
1)Open the Command Prompt on a Windows OS.
2)Navigate to the directory containing NifFinder.exe.
3)Run the following command: NifFinder.exe <path to the complete bin directory of MCR v8.0>.
4)Wait a few seconds for the program to initialize.
5)In the first window, select the directory containing the FASTA files.
6)In the second window, choose the directory containing RNAnif.mat and Rbase.mat.
7)Wait for all four processing steps to complete.
8)Done! Your results are ready.