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SPSpfam 2.3.1 Documentation

Speedup refers to the elapsed time differences between the two versions.
A speedup of 10 means that SPSpfam finished the job 10 times faster than Hmmpfam.
(i.e. A job which took ten minutes using Hmmpfam finished in one minute using SPSpfam.)
All comparison times presented here are elapsed time! The time from start to finish. These are not kernel, or partial, algorithm measurements. They are results which you should expect to achieve on a system similar to our benchmark system (see Appendix A). These relative results should be similar across all architectures and operating systems. Obviously, ther will be differences due to performance variations of different manufacturers' hardware. The speedup curve shown here should be nearly the same for all supported hardware systems.

Notice that with as few as ten input queries the SPSpfam performance improves threefold over the single query time. If you are bulk processing hundreds or thousands of amino acid queries a day you will save a significant amount of computing power and money by substituting SPSpfam for Hmmpfam.

Further Performance Considerations

As we stated earlier the performance of SPSpfam is due to many variables. The other important variable is the average length of the queries. The following graph shows the expected performance gains as a function of the length of the queries. We chose to show the performance speedup profile for input files with 16 queries.

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