Codes in this repo has been written by Eugene Gan, Ng Jing Ting and Tay Hui Yi for SP3172 - Decoding Capsule Synthesis, under Prof. Sham Lok To.

AlphaFold-Colouring with pLDDT values-

The notebook allows users to colour their structures generated from AlphaFold with the pLDDT values generated. A new PDB file with the b-factor column edited with pLDDT values will be created. Opening the file with softwares such as PyMol will allow the user to view the coloured structure.

Brief instructions

1. Change working directory to the location with all necessary files, i.e. PDB structure, pkl file
2. Provide the name of the new PDB file generated in the last cell, i.e. io.save("your_filename.pdb")

Note

• BioPython is needed to run the code

Extraction of glycosyltransferase sequences

The script, "GT_Extraction.java", allows users to extract glycosyltransferase (GT) sequences from the genomes of organisms. A new fasta file is generated with the nucleotide sequence of each GT of a particular serotype.

Brief instructions

1. Remove ID details (e.g. ID 35F_pne74 standard; DNA; UNC; 15137 BP.)
2. Indicate path to the embl file containing the serotypes genome under the variable, "file"
3. Indicate path and provide the name of the new text file generated under the variable, "fout"
4. Run the code

Note

• BioJava is needed to run the code

Translating nucleotide sequences

This notebook allows users to translate nuleotide sequences, and loop the process to translate a large number of sequences. Individual files of translated sequences will be written, which may be collated using Step 4 in the notebook.

Brief instructions

1. All files should be in FASTA format
2. All FASTA files should be in the same working directory
3. To carry out Step 4, all translated files should be in the same working directory, which ONLY contain the files to be merged.

Note

• Biopython is needed to run the code

Notes for all notebooks

• Detailed explanation and instructions are within the notebook, commented out.
• The code in all notebooks can be looped to edit multiple files at a time, though it is not included.