⚠️​ Still under heavy development!

A modern, lightweight bioinformatics toolkit for Node.js --- designed as an alternative to BioPython for the JavaScript ecosystem.

organique is a modular bioinformatics library built for JavaScript and TypeScript.
It offers tools for DNA validation, transcription, translation, and protein extraction, with a clean and intuitive API.

The project was created as part of a bioinformatics course, but it is structured as a real open-source package suitable for developers and researchers.

• DNA validation and sanitization
• DNA → RNA transcription
• Configurable codon translation
• ORF parsing
• Protein extraction from DNA strands
• Pattern Matching utilities
  • Knuth-Morris-Pratt Algorithm implementation (prefer native RegExp when possible)
• Sequence Alignment
  • Global alignment with Needleman-Wunsh
  • Local alignment with Smith-Waterman
• TypeScript-first API
• Works with Node 20+ (ESM)
• CLI application (npx organique -h) exposing some useful one-shot functions (e.g., DNA stats)
• BLAST remote computation (NCBI servers)
• Phylogenetic Analysis
  • Tree, Matrices and Phylogenetic Trees user-friendly logs
  • UPGMA algorithm implementation

⚠️​ Not yet available to the public

npm install organique

TODO

npm test

• FASTA and FASTQ file support
• RNA secondary structure tools
• Codon usage tables
• Alignment utilities
• Additional genetic codes (mitochondrial, bacterial, etc.)
• Restriction Enzymes patterns
• Expose functions and services as a REST API web server
• Add more substitution matrix for sequence alignment:
  • BENNER22, BENNER6, BENNER74, BLOSUM45, BLOSUM80, BLOSUM90, DAYHOFF, FENG, GENETIC, GONNET1992, HOXD70, JOHNSON, JONES, LEVIN, MCLACHLAN, MDM78, NUC.4.4, PAM250, PAM30, PAM70, RA0, RISLER, SCHNEIDER, STR, TRANS
• Version /streams of all the algorithms to handle huge on-the-fly processing

Contributions are welcome. Please fork the repo, create a feature branch, add tests, and submit a pull request.

MIT License.

Developed educational and research purposes, with the goal of making bioinformatics more accessible in the JavaScript ecosystem.