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Accelerated Profile HMM Searches

Figure 5

Speed benchmarks.

Each point represents a speed measurement for one search with one query against target sequences ( for the slow HMMER2 and SAM programs, for FASTA and SSEARCH), on a single CPU core (see Methods for more details). Both axes are logarithmic, for speed in millions of dynamic programming cells per second (Mc/s) on the y-axis and query length in residues on the x-axis. Panel A shows “typical best performance” speed measurements for several different programs including HMMER3, for 76 queries of varying consensus lengths, chosen from Pfam 24, for searches of randomized (shuffled) target sequences. Panel B shows a wider range of more realistic speed measurements for all 11,912 profiles in Pfam 24, on searches of real target protein sequences from UniProt TrEMBL.

Figure 5

doi: https://doi.org/10.1371/journal.pcbi.1002195.g005