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. 2008 Dec 4;37(2):463–472. doi: 10.1093/nar/gkn945

Table 10.

Average SPS and CS scores (in %) on HOMSTRAD and average SPS, CS and SCI scores (in %) on Data-set 1 of BRAliBase II by varying the parameter ω that specifies the maximum number of horizontal positions that are included to the left and to the right, and the parameter β that specifies the weight of the neighboring scores

MUMMALS on HOMSTRAD
MUSCLE on BRAliBase
ω =1 ω =3 ω =5 ω =7 ω =9 ω =3 ω =6 ω =9 ω =12 ω =15
SPS SPS
β =0.2 83.72 83.72 83.64 83.49 83.18 β =0.2 84.64 84.83 84.63 84.30 83.64
β =0.4 83.70 83.70 83.60 83.34 82.94 β =0.4 84.63 84.65 84.58 84.19 83.15
β =0.6 83.72 83.72 83.54 83.27 82.84 β =0.6 84.54 84.64 84.42 84.12 83.04
β =0.8 83.72 83.72 83.52 83.24 82.78 β =0.8 84.69 84.71 84.36 84.00 82.95
β =1.0 83.73 83.70 83.50 83.21 82.75 β =1.0 84.69 84.81 84.41 83.98 82.91
CS CS
β =0.2 79.60 79.61 79.56 79.39 79.03 β =0.2 73.84 74.20 73.92 73.42 72.52
β =0.4 79.57 79.61 79.52 79.22 78.74 β =0.4 73.92 73.93 73.85 73.31 71.81
β =0.6 79.59 79.64 79.44 79.13 78.62 β =0.6 73.67 73.92 73.54 73.16 71.48
β =0.8 79.60 79.63 79.41 79.08 78.55 β =0.8 74.03 74.03 73.47 73.03 71.27
β =1.0 79.60 79.61 79.39 79.04 78.51 β =1.0 74.03 74.00 73.57 72.90 71.22
SCI
β =0.2 73.20 74.19 74.29 74.19 73.26
β =0.4 73.34 73.96 74.02 74.11 72.83
β =0.6 73.19 73.94 73.92 74.12 72.69
β =0.8 73.28 73.79 73.64 73.97 72.41
β =1.0 73.11 73.93 73.84 74.11 72.15

For each modified algorithm and each score measure, the highest accuracy value and the values of ω and β that correspond to our chosen parameter setting that is the same across different benchmarks are in bold.