Biopython

Load GenBank file using SeqIO.

Iterate through SeqFeatures to extract CDS and Gene locations.

Translate DNA sequences to Protein using the .translate() method.

Cross-reference sequences against local databases.

Parse PDB file with PDBParser.

Identify the ligand residue object.

Loop through surrounding amino acid atoms.

Apply the Biopython distance operator (-) between atom objects.

Load multiple sequence alignment via AlignIO.

Calculate a distance matrix using the DistanceCalculator module.

Construct a tree using the DistanceTreeConstructor (e.g., UPGMA or Neighbor-Joining).

Visualize the output using Matplotlib.

Stream large FASTA files using SeqIO.index.

Filter records based on length or specific motifs.

Remove sequences containing ambiguous 'X' or 'N' characters.

Serialize to JSON for model training inputs.

Define search terms and execute Entrez.esearch.

Fetch result IDs.

Retrieve full summaries using Entrez.efetch.

Parse XML output to extract publication dates and abstracts.

Input primer sequences into Bio.SeqUtils.MeltingTemp.

Calculate Tm using Wallace, salt-adjusted, or nearest-neighbor methods.

Check for potential hairpin loops or self-dimerization.

Flag primers that fall outside the target 55-65°C range.

Import SNP data into the PopGen.GenePop module.

Calculate allele frequencies and heterozygosity.

Compute Fst and other population parameters.

Generate statistical reports for publication.