NitroBlast Project

Welcome to the TU Delft iGEM 2024 NitroBlast project repository. This repository contains all the code and data used in the project.

Repository Structure

• data/: Contains all data files
  • adk1075-data/: Data from Tyler H. Coale et al., Nitrogen-fixing organelle in a marine alga.Science384, 217-222(2024).
  • plmsearch-data/: Results from the PLM search
  • ucyn-a_enriched/: Sequence data, embeddings, alignments, and other data for UCYN-A enriched proteins
  • utp-data/: Sequence data, MEME results, HMM profiles, and other data related to the ucyn-a transit peptide
• notebooks/: Jupyter notebooks for data analysis
• scripts/: Python scripts for data processing
• results/: Final, cleaned results such as figures and tables
• JOURNAL.md: Detailed notes on the project progress

Setup

The project uses Python and conda for package management. To set up the project:

1. Clone the repository
2. Create a new conda environment: conda env create -f environment.yml
3. Activate the environment: conda activate nitroblast

Tip: micromamba is a faster alternative to conda.

External Data

• Protein embeddings for UCYN-A enriched proteins: embeddings.h5