Relative error estimates per SMART/Pfam domain. Figures A, B and C, D show the histograms of the relative errors for the HMMER2 and HMMER3 results and the SMART and PFAM domain databases respectively. The average reconstruction errors by HMMER2 were 0.0028 (SMART) and 0.0025 (Pfam) and mostly well below the 0.01 margin (or 1% of the average seed score per domain) as depicted by the vertical dashed lines. Likewise, the average reconstruction errors attributed by HMMER3 are 0.0049 and 0.0010 for SMART and Pfam domains respectively (See vertical dashed lines). They are well below the 0.05 line (or 5% of the average seed score per domain). Generally speaking, the relative errors tend being dwarfed by their respective domain-wise alignment scores for all seed sequences.