Metadata-Version: 2.1
Name: deepgoplus
Version: 1.0.0
Summary: DeepGOPlus function predictor
Home-page: UNKNOWN
Author: Maxat Kulmanov
Author-email: maxat.kulmanov@kaust.edu.sa
License: Apache 2.0
Download-URL: https://github.com/bio-ontology-research-group/deepgoplus/archive/v1.0.0.tar.gz
Description: # DeepGOPlus: Improved protein function prediction from sequence
        
        DeepGOPlus is a novel method for predicting protein functions from
        protein sequences using deep neural networks combined with sequence
        similarity based predictions.
        
        This repository contains script which were used to build and train the
        DeepGOPlus model together with the scripts for evaluating the model's
        performance.
        
        ## Dependencies
        The code was developed and tested using python 3.6.
        To install python dependencies run:
        pip install -r requirements.txt
        
        ## Data
        * http://deepgoplus.bio2vec.net/data/ - Here you can find the data
        used to train and evaluate our method.
         * data.tar.gz - Data required to run predict.sh script
         * data-cafa.tar.gz - CAFA3 challenge dataset
         * data-2016.tar.gz - Dataset which is used to compare DeepGOPlus with
           GOLabeler and DeepText2GO
        
        ## Scripts
        The scripts require GeneOntology in OBO Format.
        * uni2pandas.py - This script is used to convert data from UniProt
        database format to pandas dataframe.
        * deepgoplus_data.py - This script is used to generate training and
          testing datasets.
        * deepgoplus.py - This script is used to train the model
        * evaluate_*.py - The scripts are used to compute Fmax, Smin and AUPR
        
        ## Running
        * Download all the files from http://deepgoplus.bio2vec.net/data/data.tar.gz and place them into data folder
        * Install [diamond](https://github.com/bbuchfink/diamond) program on your system (diamond command should be available)
        * run predict.sh <input_fasta_filename> <results_filename>
        
        The online version of DeepGOPlus is available at http://deepgoplus.bio2vec.net/
        
        ## Citation
        
        If you use DeepGOPlus for your research, or incorporate our learning algorithms in your work, please cite:
        Maxat Kulmanov, Robert Hoehndorf; DeepGOPlus: Improved protein function prediction from sequence, Bioinformatics, https://doi.org/10.1093/bioinformatics/btz595
        
        
Platform: UNKNOWN
Requires-Python: >=3.6, <3.7
Description-Content-Type: text/markdown
