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The weight assigned to the secondary structure prediction model. The overall score at each position in the provided sequence is composed of three scores: the secondary structure prediction score, the side chain entropy score and the BLAST search score.

By default the weight for the secondary structure prediction is 1 and equivalent to the Blast search weight, while the side entropy weight is 0.5 (since the cluster pattern search provides additional emphasis for the side entropies).

These weight may be adjusted if one wished to give more emphasis on one of the three models described above. To give the secondary structure more consideration, increase this weight to say 1.5 or 2.0.