ag4349/msa-webgpu
Private, browser-native protein MSA search with WebGPU - ag4349/msa-webgpu
0 stars · 0 forks
README
MSA WebGPU A small browser-based protein search and MSA tool. Database scoring runs with WebGPU, and local FASTA files stay on your machine. Running locally Requires Node.js 20+ and a browser with WebGPU support. npm ci npm run dev The local FASTA option works as-is. The Swiss-Prot options need database packs generated separately. How it works The GPU runs an ungapped BLOSUM62 search over the database. The best candidates are realigned on the CPU with Smith-Waterman-Gotoh, filtered, and exported as A3M, FASTA, or Stockholm. This is a query-centered star alignment. It is not a replacement for MMseqs2 and does not calculate E-values. Swiss-Prot data npm run swissprot:fetch npm run swissprot:pack npm run swissprot:pack20k To pack another FASTA file: npm run db:shard -- proteins.fasta public/packs/my-database 20000 The generated directories go under public/packs. Set VITE_DATABASE_ROOT if they are hosted somewhere else. The file format is described in DATABASE_FORMAT.md. Swiss-Prot data is available from UniProt under CC BY 4.0. Checks npm test npm run build Shader validation is optional and requires naga: npm run validate:wgsl Production deployments need HTTPS for WebGPU and persistent browser storage. License MIT