SPSpfam 2.3.1 Documentation
SPSpfam shows dramatic performance gains for average query lengths of 200 amino acids or less. For ten aa length queries the performance gain was 57! At 200 aa length queries the speedup is still about one order of magnitude greater than Hmmpfam. This is significant, as SPSpfam gives you the same throughput on ten processing nodes as Hmmpfam gives you on one hundred nodes! The hardware cost savings for equivalent throughput can be enormous.
Appendix A (Benchmark Conditions)
System: Dual processor 2.2 Ghz Pentium
IV xeon chip set.
Memory: 1 Gbyte DDR Ram
OS:
Red Hat Linux version 7
Both processors were used for Hmmpfam and SPSpfam.
The HMM library was Pfam_ls 8.0 (5049 models)
All runs on both codes were timed on subsequent
runs after one short initial run.
The Hmmpfam binary from the HMMER Intel Linux distribution was used
for the comparisons.
The Unix time command was used to time
all runs.
Appendix B (Independent Work)
See the poster by Martin Gollery, "A Comparison of HMMPfam Implementations" for an independent comparison of SPSPfam 2.2g at www.unr.edu/BRIN/pfamposter.pdf
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