The running time of the pipeline depends significantly on the size of the data set, the number of features requested for each bio-sequence, the success of the search, the number of concurrently executing threads, and the computing power of the machine executing the code. The longest step in the execution of the pipeline is BLAST on a standard Linux box. In fact, the running time of all other steps in the pipeline combined, is insignificant to the running time of the BLAST step. For the ISB internal setup of BIOSAP, we are working on employing the GeneMatcher super-computer for the execution of this step.