sc-git1/ogtpredmodels

Copyright © 2022-2023 Sophie Colette. All Rights Reserved.

Code accompanying my Master's thesis in Bioinformatics

Title: Machine learning for organism growth temperature prediction and application of resampling methods to improve imbalanced data

Promotor: prof. Vera van Noort

Supervisor: Jaldert François

Each folder contains the code for part of the workflow:

1. Mining: Web mining and integration with existing OGT databases
2. Database QC: Quality assessment of the databases
3. Genome retrieval: Extracting genomes for the species with available growth temperature
4. Genome Annotation: Proteome predictions with Prokka and Augustus
5. Stability: Feature stability analyses for the AA descriptors on protein and proteome level
6. Data Analysis: PCA and correlation analyses
7. Embeddings: Extraction of ProtTrans and UniProt embeddings
8. Modelling: linear regression models + XGBoost, SVR and RF both without (random split and phylogenetic split) and with resampling
9. Agreement statistics: Comparison of the predicted proteomes with UniProt reference proteomes