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Figure 9 | BMC Bioinformatics

Figure 9

From: Accurate statistics for local sequence alignment with position-dependent scoring by rare-event sampling

Figure 9

Fit parameters for different alignment models. Fit parameters for score distributions P (S|# of helices) for the (HMM) with a fixed query length L Q = 348 and various subject lengths L S . Both shape parameters λ and λ2 decrease with increasing number of helices. The dependency on the subject length is stronger for λ2 than for λ. For L S >L Q the dependency of λ2 on the subject length is only of marginal order. The bars show the distribution of the number of transmembrane helices obtained by direct simulations of the (HMM). (c),(d): The L S /L Q dependency of λ and λ2 extracted from the same data as (a),(b). The lines are guide to the eyes only. Dashed lines show the corresponding scaling behavior for the (FQRS) and (RQGS) models. The result for n = 2, that has been obtained from the high probability regions (see text), is indicated by dotted lines.

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