Start here: hiv.py
This is a small hack of mine I put together to learn more about reverse engineering the DNA and implementation of the central dogma of molecular bio in code.
utils.py is a custom module containing useful functions written from scratch.
transcription function converts DNA to mRNA. rna_translation function converts mRNA sequence to a chain of amino acids which also can be viewed in short-form or full-length-forms using translation_shortform and translation_fullform functions respectively.
Proteins are being stored in a FASTA file (check proteins.fasta for example) for all orders of ORFS's (first, second and third) in both forward and reverse chains.
dna_features_viewer module is being used to visualise the DNA. Check example here
visualize.py uses ESM1B (an LLM for proteins) to convert amino acid sequences into PDB format and then uses ProDy & Matplotlib to 3d visualise the protein strand.
Note : only the largest protein strand of each ORF is being plotted while the length of protein strand also being under 400 due to ESM1B API constraint.
3dmol.ipynb uses py3Dmol to individually visualise better model of all the ORFs (dna + rna, all orders)
hiv.py contains an implementation of all the functions over the genome of sequence of HIV-1. The accuracy is quite decent so far, majority of proteins have been verified from the official site