Briefly, the method employed in the SUPFAM+ database first relates Pfam families (with or without known structures) to SCOP superfamilies using a rigorous profile-profile alignment method, AlignHUSH [ 29].
Previously developed rigorous profile-profile comparison methods [ 18- 22] use very sophisticated models of profile representation and of course our algorithm can not compete with these methods if it is applied to detect remote homologies.
When it is applied to detect weak similarity between protein families, PHOG-BLAST is less precise than rigorous profile-profile comparison method, though it runs much faster and can be used as a hit pre-selecting tool.
To test the PHOG-BLAST procedure, we compared it with PSI-BLAST [ 7], a well-known algorithm for fast profile search, and with COMPASS [ 18], one of the best rigorous profile-profile comparison methods.
This observation together with our experience of using PHOG-BLAST when we built the PHOG database [ 4] demonstrates that PHOG-BLAST used in this setting does not create false positive BBHs and finds 5%% less BBHs than rigorous profile-profile methods.
In our previous study, we performed a rigorous profiling of eThread in terms of time-to-solution and memory footprint, focusing on the optimal utilization of resources provided by homogeneous high-performance computing (HPC) clusters [ 28].
Because many factors such as RNA isolation, labeling and hybridization methods affect the quality of microarray data, pooling data from different experiments does not allow for a rigorous expression profiling analysis.
More in-depth biochemical studies (specific degradation products) and rigorous expression profiling (RNA-seq) are planned in order to clarify the exact function of this, or other, CYP450s involved in terpene interactions.
The rigorous analysis of temperature profiles in the monolith structure facilitates future extension of the model to include homogeneous and heterogeneous reaction terms.
To make performance profiling more rigorous, sports scientists must determine a typical trajectory for each sport and each event by studying data from hundreds, even thousands of careers, says Berthelot.
We make a rigorous exploration of the profiles of off-diagonal components of frequency-dependent linear (αxy, αyx), first nonlinear (βxyy, βyxx), and second nonlinear (γxxyy, γyyxx) polarizabilities of quantum dots driven by Gaussian white noise.
