BioRazer

A Python package for analyzing various biological information, built from practical lab experience. Install with pip and you're ready for common bioinformatics analysis work.

Features

• Protein sequences — Translation, reverse translation, codon/protein dictionaries
• Multiple Sequence Alignment (MSA) — Generate MSA via ColabFold MMseqs2 API, visualize coverage, analyze amino acid frequencies
• Structure analysis — Static analysis (contacts, hydrogen bonds, surface selection), dynamic trajectory analysis (MD trajectory view, XVG/XPM plots)
• Database access — Query AFDB, RCSB PDB, UniProt, Ensembl
• Rotamer libraries — Read external side-chain rotamer databases: PyMOL's bundled Dunbrack pickles (sc_bb_ind / sc_bb_dep) and Rosetta's Dunbrack 2002 / Shapovalov 2010 text libraries
• Protein design — Sequence design, library generation, single test entries

Installation

pip install biorazer

Dependencies

• Python >= 3.11
• biotite, numpy, scipy, matplotlib, hydride, umap-learn, rcsb-api
• tabulate (for formatted output)

Development

# Install with dev and test dependencies
poetry install --with dev,test

# Or using pip with test dependencies
pip install biorazer
pip install pytest pytest-cov

Usage

ColabFold MSA via MMseqs2 API

Generate protein MSA by calling the ColabFold public API — zero additional dependencies, pure stdlib:

from biorazer.sequence.protein.analysis.alignment.query import run_search

# Single-chain MSA (unpaired, default)
files, _ = run_search(
    ["MTSENLYFQGAMG..."],
    out_dir="msa_out/",
)

# Multi-chain paired MSA (for AF3 multimers)
files, _ = run_search(
    ["CHAIN1_SEQUENCE", "CHAIN2_SEQUENCE"],
    out_dir="msa_out/",
    pair_mode="paired",
    pair_strategy="greedy",   # or "complete"
)

Output: A3M files (uniref.a3m, bfd.mgnify30.*.a3m, pair.a3m) ready for downstream folding pipelines. Supports template search (--templates) and custom MMseqs2 server URLs.

MSA Visualization

from biorazer.sequence.protein.analysis.alignment import plot_msa

fig, ax = plot_msa(
    sequences=["MTSENLYFQG", "MTSENLXFQG"],
    labels=["Wild-type", "Mutant"],
)
fig.savefig("msa_plot.png")

Testing

pytest tests/ -v

Tests cover: FASTA parsing, sequence validation, A3M merging, and module constants. All tests are pure (no network required).

Project Structure

biorazer/
├── access/         # External database APIs (AFDB, RCSB, UniProt, Ensembl)
├── database/       # Reference data & external-library readers
│   └── molecule/   #   per-molecule data
│       ├── atom/       #     vdW radii, charges
│       ├── bond/       #     bond length / angle / dihedral
│       ├── icoor/      #     internal-coordinate topology & templates
│       └── rotamer/    #     external rotamer readers, split by source
│           ├── rosetta/    #   Dunbrack 2002 / Shapovalov 2010 text libraries
│           └── pymol/      #   PyMOL's bundled Dunbrack pickles
├── design/         # Protein design tools
├── sequence/       # Sequence analysis
│   ├── nucleotide/
│   ├── protein/
│   ├── analysis/alignment/   # MSA analysis & plotting
│   │   └── scripts/          # MSA visualizer, analyzer
│   └── translation/
├── structure/      # Structure analysis & I/O
└── util/           # Utility modules (dictionaries)

License

This project is licensed under the MIT License.

This project is intended for academic and research use.