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:

• <i>RBP_database.csv</i> contains the collected RBP sequences as described in Materials & Methods.

• <i>RBP_functions.py</i> is a Python script containing all the necessary manually implemented functions for the various analyses carried out in this study.

• <i>RBP_alignment.jl</i> is a Julia script used to compute pairwise alignments between the sequences to explore the diversity and assess redundancy in the database.

• <i>RBP_alignmentscores.txt</i> is .txt file containing the alignment scores if you prefer not to compute them with the provided Julia script.

• <i>RBP_host_prediction.ipynb</i> 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.