Figure 3.

Generating the proposal alignment. This figure illustrates the stochastic sequence aligner. In the deterministic fill-in process, the three scores are s1, s2 and s3, hence the value in this cell is max{s1, s2, s3}. In the stochastic traceback phase, the three neighbor cells are choosen with probabilities proportional to exp(αsi), where α > 0 is a scaling parameter. The chosen traceback path corresponds to the proposed alignment in the usual way.

Lunter et al. BMC Bioinformatics 2005 6:83   doi:10.1186/1471-2105-6-83
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