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A search engine for DNA/RNA/Protein sequences using JCL (JavaCá&Lá)
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A search engine for DNA/RNA/Protein sequences using JCL (JavaCá&Lá)

JavaCa&La Sequence Search Engine or simply JCL-SSE is a tool that runs over a cluster of multicore computers, enabling a huge number of protein and DNA sequences alignments. In summary, it makes simple the utilization of JCL ( High Performance Computing (HPC) middleware Application Programming Interface (API) and for that it implements a Graphical User Interface (GUI) where users can index, query and rank similar sequences. Internally, the alignment implements the Smith-Waterman algorithm with the Gotoh improvement to perform the pairwise alignments. The FASTAReader and BioJava Libraries are employed to read the data from a FASTA file database and process both Protein and DNA sequences.

How do I Run It ?

It is necessary, first, to start a JCL cluster. In the JCL website there are all the necessary guides for JCL deployment and development. In sequence, you have to follow the steps:

You must import the JCL-SSE Eclipse project. File -> Import -> Existing Projects Into Workspace.

After everything is set up, you can run the in the GUI folder.

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