One of the main problems of bioinformatics is sequence alignment. Sometimes, as when aligning RNA sequences, it is necessary to find long deletion gaps which is something most classic alignment algorithms cannot do. To make sure such gaps get found, we use concave penalty function. Calculating value of concave function in specific point is complex and slow process so we approximate it with a certain number of affine functions. Most popular algorithm allowing for long gaps is Gotoh's algorithm. Vectorization is technology supported by most modern processors and it allows us to do simple operations such as addition on bigger data at the same time. Because of that, vectorization can efficiently speed up sequence alignment process. We developed tool called OSALG, an implementation of Gotoh's algorithm (and its variations).
To install OSALG run commands:
git clone --recursive https://github.com/RJPenic/OSALG
cd OSALG
mkdir build
cd build
cmake .. -DCMAKE_BUILD_TYPE=Release
makeAfter installation, executable file will be located in /build/bin folder. To use OSALG run:
cd bin
./OptSeqAlignmentLongGaps reads.fasta references.fastaIt is highly recommended to use '--vector' option for improved results and faster execution.
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