Statistical Significance of Alignments

Eshmahng the statistical significance of alignments (by shuffling) Sechon 7 21... 

Alexandrov, N. N. and V. V. Solovyev, Statistical significance of ungapped sequence alignments. Pac Symp Biocomput, 1998 p. 463-72. 

In the last example, we used RNAalifold essentially to detect structural RNAs within long aligned sequences. The method does not, however, provide a good measure for the statistical significance of predicted consensus structures. For example, it is difficult to decide whether a predicted structure is functionally important or just incidental. 

The 2D conductance-distance histogram shows the logarithm of the experimentally obtained conductance in units of Go plotted vs distance [54, 63, 142], The distance axis is normalized with respect to the atomic contact rupture, to align the experimental traces to a common point. Examples are z = 0 at G = 0.7 G0 [54], Individual conductance-distance traces obtained in this manner are binned in 2D space (usually 1,000 x 1,000 bins), and then all individual 2D histograms are added together. The result represents statistically significant conductance-distance trends. 

Large segments contain identical residues, the value (the assessment of the statistical significance based on the extreme value distribution) of the alignment is statistically highly significant, the active site is conserved, and so we tentatively classify it as a "probable mitochondrial NUCLEASE."... 

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