LAMBS - Local Analysis of mAb Sequences

About 🐑

Completely free, private, and self-contained analysis of monoclonal antibody (mAb) sequences. Analyze gene segments, germline mutations, CDRs, developability liabilities, and more.

The best part? It's a single html file that runs offline in a web browser, which means no installation, no programming, and your sequences stay private!

Code is open source, permissively licensed under Apache 2.0, and available at https://github.com/dcroote/lambs.

Usage

1. Download index.html from the latest release
2. Open index.html in your web browser
3. Enter your VH and VL amino acid sequences and click "Analyze"
4. View the results
5. Make better antibodies for humankind!

Screenshot

Developer notes

Testing

node test.js

Populating the V_GENE_DB object in index.html

python3 populate_germlines.py

Background: IgBLAST used to annotate CDRs

This was run in a separate directory containing IgBLAST v1.22.0 and IMGT sequences. For mouse, human was replaced with mouse in all arguments. Assumes the database files (outputs of makeblastdb) were in the db directory. Assumes the auxiliary data is in the optional_file directory (standard, comes with IgBLAST).

./bin/igblastn \
    -germline_db_V db/human_V.fasta \
    -germline_db_D db/human_D.fasta \
    -germline_db_J db/human_J.fasta \
    -num_alignments 1 \
    -ig_seqtype Ig \
    -organism human \
    -outfmt 19 \
    -auxiliary_data optional_file/human_gl.aux \
    -domain_system imgt \
    -query db/human_V.fasta \
    -out igblast_human_V.tsv

Background: Initial prompt and plan

For those curious, see .cursor/initial.prompt.md and .cursor/initial.plan.md for the original prompt and plan, respectively.