sword

KO | EN

gitlite — search

#javascript #python #hacktoberfest #react #ai #typescript #llm #go #golang #android #machine-learning #rust #deep-learning #linux

★ 26 Open GitHub ↗

SWORD - a highly efficient protein database search

Download

Download Latest Version (.zip)

// repository documentation

Was this content helpful?

★ 0 (0 ratings)

# SWORD

[![Latest GitHub release](https://img.shields.io/github/release/rvaser/sword.svg)](https://github.com/rvaser/sword/releases/latest)
[![Published in Oxford Bioinformatics](https://img.shields.io/badge/published%20in-Oxford%20Bioinformatics-blue.svg)](https://doi.org/10.1093/bioinformatics/btw445)

SWORD (Smith Waterman On Reduced Database) is a fast and sensitive software for protein sequence alignment. SWORD consists of two steps, first being a heuristic and the second being optimal alignment phase. In the first step, for each query, it reduces the database to A sequences that score best with the query, which are in the second step aligned to the query using [OPAL](https://github.com/Martinsos/opal) library. SWORD utilizes multithreading.

## DEPENDENCIES

### LINUX and MAC OS

Application uses following software:

1. SSE4.1 or higher
2. gcc 4.8+
3. cmake 3.2+

## INSTALLATION

### LINUX

To build SWORD run the following commands from your terminal:
```bash
git clone --recursive https://github.com/rvaser/sword.git sword
cd sword/
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make
```

After running make, an executable named `sword` will appear in the `build` directory.

#### Troubleshooting

If you have cloned the repository without `--recursive`, run the following commands:
```bash
git submodule init
git submodule update
```

The software should also run on MAC OS, but it was not tested in that environment.

## EXAMPLES

All examples assume that make has been run and that SWORD was successfully compiled.
Simplest protein FASTA database search can be executed using the following command:

```bash
./sword -i <query> -j <database>
```
This will run a search using the default, sensitive mode.

For the complete list of parameters and their descriptions run the following command:

```bash
./sword -h (or ./sword --help)
```

## Contact information

For additional information, help and bug reports please send an email to: robert.vaser@fer.hr.

## Acknowledgement

This work has been supported in part by Croatian Science Foundation under the project UIP-11-2013-7353 and in part
by the Foundation of the Croatian Academy of Sciences and Arts.

sword

Download

Today's picks

Was this content helpful?

Recent Feedback

sword

Download

Today's picks

Was this content helpful?

Recent Feedback

Download README