Fig. 6
From: HH-suite3 for fast remote homology detection and deep protein annotation
Speed comparisons. a runtime versus query profile length for 1644 searches with profile HMMs randomly sampled from UniProt. These queries were searched against the PDB70 database containing 35 000 profile HMMs of average length 234. The average speedup over HHsearch 2.0.16 is 3.2-fold for SSE2- vectorized HHsearch and 4.2-fold for AVX2-vectorized HHsearch. b Box plot for the distribution of total runtimes (in logarithmic scale) for one, two, or three search iterations using the 1644 profile HMMs as queries. PSI-BLAST and HHMER3 searches were done against the UniProt database (version 2015_06) containing 49 293 307 sequences. HHblits searches against the uniprot20 database, a clustered version of UniProt containing profile HMMs for each of its 7 313 957 sequence clusters. Colored numbers: speed-up factors relative to HMMER3