JCL Sequence Search Engine (JCL-SSE)

 

What does the sample do?

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 (www.javacaela.org) 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 SearchMainWindow.java in the GUI folder.

 

How do I use it?

If you followed the previous steps correctly, the main window should pop up.  

Fig.1 Main JCL-SSE window

After that , you can load the sequence. The sequence must be a FASTA file containing only ONE SINGLE SEQUENCE . Then , you can load the database. The database must be a single folder containing the FASTA files inside it. The FASTA files available for comparison will be displayed in the "Sequences From" dropdown.

Next, you just have to select the number of results that you want to be displayed, i.e., the top-k rank of sequences. Before you click in the Submit button, be sure that your screen looks similar to Fig.2.

Fig.2 One possible configuration for JCL-SSE

 

Fig.3 Top-k most similar sequences displayed 

 

Finally , you have the most similar sequences of a database displayed. If you want to know more details about the top-k similar sequences found, you can just click in the desired sequence and than click in the "Details" button. The following screen will be displayed.

 

Fig.4 Detailed information about a specific sequence

 

The "Display structure"  and "NCBI link" buttons will be a available in future versions of JCL-SSE.

 

Questions or comments, where can I go?

 

Questions about the API or about the codes of this application? See our Programming Guide and Installation Guide.

If you have any questions, please contact the JCL team.