The BLAST algorithm has three major variations in common use. BLASTN compares a DNA sequence against a DNA database. BLASTP compares a protein sequence against a protein database. BLASTX compares a DNA sequence against a protein database by running the algorithm six times for the six different ways of translating a DNA sequence into a protein sequence. Of these three algorithms, BLASTN takes the least amount of time because it uses the simplest cost function for mismatches. BLASTP and BLASTX take a similar amount of time for each search, but BLASTX is several times slower because it does six searches for each sequence.
The machines used in the experiments are listed in
Table 
.
Table: SMP machine characteristics
The experiments are designed in two stages. The first stage tests the first two hypotheses: that BLAST run time is proportional to sequence length and that performance is independent of sequence content. The second stage measures the throughput and response time performance of BLAST on each of the three multiprocessors. The results from the first stage are used to determine the sequences used in the second stage.
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