Biopython Bio

Bioinformatics operations using Biopython.

When to Use

• Reading/writing sequence files (FASTA, GenBank)
• Running BLAST searches (local or remote NCBI)
• Sequence alignment and manipulation
• Parsing PDB protein structures
• Phylogenetic tree construction
• Querying NCBI Entrez databases

When NOT to Use

• Clinical genomics or variant calling (use GATK, bcftools)
• RNA-seq differential expression (use DESeq2, edgeR)
• Genome assembly (use SPAdes, Canu)
• Molecular dynamics simulations (use GROMACS, OpenMM)