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 library. SWORD utilizes multithreading.

Application uses following software:

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

To build SWORD run the following commands from your terminal:

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.

If you have cloned the repository without --recursive, run the following commands:

git submodule init
git submodule update

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

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:

./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:

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

For additional information, help and bug reports please send an email to: [email protected].

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.