2.5. Calculation of Statistical Significance for maxV(n1)
This protocol is extracted from research article:
Multiple Alignment of Promoter Sequences from the Arabidopsis thaliana L. Genome
Genes (Basel), Jan 21, 2021; DOI: 10.3390/genes12020135

We used the Monte Carlo method to estimate the statistical significance of maxV(n1). Sequence S was randomly shuffled to obtain 200 random sequences. Then, matrix maxW was included in the Q set described in Section 2.2, which allowed taking into account the effectiveness of maxW alignment with random sequences. Then, each of these sequences were treated as described in Section 2.2, Section 2.3, Section 2.4 and maxW was calculated for each, producing 200 maxV(n1). Then, the mean maxV(n1)¯ and variance D(maxV(n1)) were calculated and used to compute Z:

where maxV(n1) was calculated for sequences S1 and S in Section 2.4.

Z was obtained for each MSA and the average Z value for random S sequences was estimated according to Formula (7) after each sequence had been subjected to the procedures described in Section 2.2, Section 2.3, Section 2.4 and here. As a result, the mean Z = 1.8, and we can assume that the MSA is non-random at Z > 6.0.

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