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The methods in STAMP can be selected by specifying the column comparison metric and alignment method [7].
Analysis of variance was followed by post-test column comparison (Tukey's test).
In TOMTOM analysis, the TRANSFAC database was selected and the Pearson correlation coefficient was employed to survey the Motif Column Comparison Function.
The phylogenetic tree of LexA-binding sites in cyanobacteria, B. subtilis, α-proteobacteria and E. coli K12 was generated by the STAMP web tool [ 42] with the default alignment parameters: Pearson correlation coefficient for column comparison metric; ungapped Smith-Waterman for pair-wise alignment.
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This approach provides an initial description of trends however effects are confounded – both age and cohort effects appear in column comparisons; cohort and period effects in row comparisons; and age and period effects in diagonal comparisons.
This was also a relatively transient population, with as many residents who had lived for 5 or more years in the neighborhood as those that had just moved in the last 5 years.> -wrap-foot> comparisonsarisofs of 0 13 unhealthy days a month vs. 14 or more unhealthy days.
Current methods for motif comparison typically involve a similarity metric for column-to-column comparison and a method to find the optimal position alignment between the two compared motifs [8].
The majority of current methods for motif comparison involve a similarity metric for column-to-column comparison and a method to find the optimal position alignment between the two compared motifs.
Statistical analysis was performed with GraphPad Prism 5 using a one-way ANOVA with post hoc Tukey pairs of columns comparison test.
Analysis of variance was used to compare multiple columns, and t-tests were used for two-column comparisons (the Mann–Whitney).
Here we presented a novel metric named SPIC (Similarity with Position Information Contents) with better performance for column-to-column motif comparison.
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