https://github.com/dimiboeckaerts/BacteriophageHostPrediction
Code and database related to our manuscript "Predicting bacteriophage hosts based on receptor-binding proteins"
https://github.com/dimiboeckaerts/BacteriophageHostPrediction
Last synced: about 2 months ago
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Code and database related to our manuscript "Predicting bacteriophage hosts based on receptor-binding proteins"
- Host: GitHub
- URL: https://github.com/dimiboeckaerts/BacteriophageHostPrediction
- Owner: dimiboeckaerts
- License: mit
- Created: 2019-12-03T12:52:39.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2023-11-02T21:54:43.000Z (over 1 year ago)
- Last Synced: 2025-03-20T05:35:48.750Z (about 2 months ago)
- Language: Jupyter Notebook
- Homepage:
- Size: 10.4 MB
- Stars: 12
- Watchers: 2
- Forks: 4
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-virome - BacteriophageHostPrediction - Computational methods for phage-host prediction. [Python] (Host Prediction / RNA Virus Identification)
README
# Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins
This repository contains the code and database related to our manuscript "Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins", published in Scientific Reports (January 2021). This research is funded by a PhD fellowship strategic basic research from the Research Foundation – Flanders (FWO), grant number 1S69520N.
Access the research paper via the following link: https://www.nature.com/articles/s41598-021-81063-4
More specifically, this repository contains the following files:
* RBP_database.csv contains the collected RBP sequences as described in Materials & Methods.
* RBP_functions.py is a Python script containing all the necessary manually implemented functions for the various analyses carried out in this study.
* RBP_alignment.jl is a Julia script used to compute pairwise alignments between the sequences to explore the diversity and assess redundancy in the database.
* RBP_alignmentscores.txt is .txt file containing the alignment scores if you prefer not to compute them with the provided Julia script.
* RBP_host_prediction.ipynb is an IPython notebook containing all the analyses, model constructions and evaluations described in Materials & Methods.
Important notice: the code in this repository is provided as is and is no longer under active maintenance. Thank you for understanding.