NCBI BLAST Java Interface

NCBI BLAST Java Interface is the Java implementation of the NCBI Blast documentation. The toolkit is free and it is subject to no support at any level. However, you can always report me the problems and I will try to fix the code. Please send me back the updated code if you happened to improve it.


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Binary jar file
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Documentation

You need to instantiate an instance of PutCommand class to submit your queries to NCBI Blast server. The documentation on NCBI Blast site explains what the parameters are.

For example:

PutCommand put_command = new PutCommand();                  put_command.setQuery("VYCVFLGFEVFVIYSFLIETRYTPMEEIAKYFDGDSAVD");         put_command.setProgram("blastp");         put_command.setIdentityPrecision(100);

Next, you will need to create a GetCommand to recieve and interpret the results. You will usually need to extends the GetCommand class and implement the parseResults(Reader in) method that is where you recieve the results. For example, BioJava API comes with a great collection of classes that interpret Blast XML files into Java Object. You may refer to BioJava API documentation page for more information.

After that, you need to create and instance of the Runner class and it will handle the communication with the NCBI Blast server.

Runner runner = new Runner(put_command, get_command);         runner.start();

and enjoy!