# pairwasm_alignment

> Experiment. Performs global and local pairwise sequence alignment through WebAssembly.

Latest version **0.2.1** (published 2024-01-28) · MIT license · 0 weekly downloads

## Install

```sh
npm install pairwasm_alignment
pnpm add pairwasm_alignment
yarn add pairwasm_alignment
bun add pairwasm_alignment
```

## Health

**Score 25/100 (F)** — status: abandoned.

Positive: has types; esm support; no vulnerabilities.

Warnings: low downloads; pre 1.0.

Negative: abandoned; low maintenance score.

## Facts

| | |
|---|---|
| Version | 0.2.1 |
| Published | 2024-01-28 |
| First published | 2024-01-20 |
| Weekly downloads | 0 |
| License | MIT |
| TypeScript types | bundled |
| Module format | ESM + CommonJS |
| Dependencies | 0 |
| Unpacked size | 93 KB |
| Known vulnerabilities | 0 |
| Install scripts | no |
| GitHub stars | 2 |
| Maintainers | hdescobarh |
| Keywords | sequence alignment, pairwise alignment, bioinformatics, WebAssembly |

## Links

- npm: https://www.npmjs.com/package/pairwasm_alignment
- Repository: https://github.com/hdescobarh/pairwasm_alignment
- Homepage: https://github.com/hdescobarh/pairwasm_alignment#readme
- Issues: https://github.com/hdescobarh/pairwasm_alignment/issues
- npm.io page: https://npm.io/package/pairwasm_alignment

## Alternatives

- [mobx-react](https://npm.io/package/mobx-react.md) — 2.8M weekly downloads
- [rc-tree](https://npm.io/package/rc-tree.md) — 2.6M weekly downloads
- [@react-oauth/google](https://npm.io/package/@react-oauth/google.md) — 1.3M weekly downloads
- [@wagmi/connectors](https://npm.io/package/@wagmi/connectors.md) — 877.0K weekly downloads
- [vee-validate](https://npm.io/package/vee-validate.md) — 836.4K weekly downloads

## Recent versions

- 0.2.1 (latest) — 2024-01-28
- 0.2.0 — 2024-01-28
- 0.1.0 — 2024-01-20

## README

# pairwasm_alignment

![Rust](https://img.shields.io/badge/-Rust-B7410E?logo=rust&logoColor=28282B&labelColor=white)
![WebAssembly](https://img.shields.io/badge/-WebAssembly-654FF0?logo=webassembly&logoColor=654FF0&labelColor=white)
![npm](https://img.shields.io/badge/-npm-CC3534?logo=npm&labelColor=white)
![Experimental](https://img.shields.io/badge/stability-experimental-orange)
![License](https://img.shields.io/badge/license-MIT-blue)

WebAssembly performance, portability, and interoperability could bring the power of the Cloud to Bioinformatics and Computational Biology, facilitating collaboration among researchers and enhancing reproducibility.

This experiment is a WebAssembly pairwise sequence alignment module written in Rust 🦀. It implements the classic Needleman-Wunsch and Smith-Waterman.

## Crate documentation and Demonstration

The WASM module use is straightforward since it only exposes a single function; read the next section for details. Also, you can check the Rust crate [documentation here](https://hdescobarh.github.io/pairwasm_alignment/pairwasm_alignment/).

I also deployed an online demonstration that runs __locally__ and on __your browser__. Be aware that Smith-Waterman and Needleman-Wunsch are dynamic programming algorithms and have [quadratic time performance](https://en.wikipedia.org/wiki/Big_O_notation). __Do not__ use the demo for long sequences.

</br>

[__Check the demo__ </br>![pairwasm_alignment](image.png)](https://hansescobar.com/en/demo/pairwasm)

## Releases and how to use them

The module is offered in two flavors:

- [npm Module](https://www.npmjs.com/package/pairwasm_alignment)

The wasm module itself is natively an ES module [^1]. It needs a Bundler. Only Webpack offers total compatibility and other bundlers will require additional configurations.

- [Web](https://github.com/hdescobarh/pairwasm_alignment/releases)

It can natively be included on a web page, and doesn't require any further postprocessing [^1].

For example,

```typescript
import init, { do_protein_alignment } from "./wasm_module/pairwasm_alignment.js";

export async function run(
  string_1: string,
  string_2: string,
  open_cost: number,
  extend_cost: number,
  substitution_matrix: number,
  algorithm: number) {
  await init();
  return do_protein_alignment(
    string_1,
    string_2,
    open_cost,
    extend_cost,
    substitution_matrix,
    algorithm
  );
}
```

Then the *run* function can be imported normally in any script.

## Known issues

- Using local alignment can give suboptimal alignments.
</br></br>

--------

[^1]: [Deploying Rust and WebAssembly](https://rustwasm.github.io/docs/wasm-bindgen/reference/deployment.html#deploying-rust-and-webassembly).

## Bibliography

- Chao, J., Tang, F., & Xu, L. (2022). Developments in Algorithms for Sequence Alignment: A Review. Biomolecules, 12(4), 546. <https://doi.org/10.3390/biom12040546>
- Masek, W. J., & Paterson, M. S. (1980). A faster algorithm computing string edit distances. Journal of Computer and System Sciences, 20(1), 18–31. <https://doi.org/10.1016/0022-0000(80)90002-1>
- Needleman, S. B., & Wunsch, C. D. (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology, 48(3), 443–453. <https://doi.org/10.1016/0022-2836(70)90057-4>
- Smith, T. F., & Waterman, M. S. (1981). Identification of common molecular subsequences. Journal of Molecular Biology, 147(1), 195–197. <https://doi.org/10.1016/0022-2836(81)90087-5>
- Smith, T. F., Waterman, M. S., & Fitch, W. M. (1981). Comparative biosequence metrics. Journal of Molecular Evolution, 18(1), 38–46. <https://doi.org/10.1007/BF01733210>

---
_Source: https://npm.io/package/pairwasm_alignment · Machine-readable twin of the npm.io package page. Health data is recomputed on every publish._