Improvement of alignment is evaluated by to two metrics known as morphology alignment score and correlation coefficient.
A combination of protein sequence alignment, and the correlation score with the subtype that gave most significant alignment with other subtypes was used to identify invariant regions.
Sheet 1: Alignment statistics and correlations between the different datasets, calculated from RPM using the unique gene set only.
On A. baylyi, OV performed relatively well, based on CDS alignments and Pearson correlation coefficients, whereas in B. subtilis, the results were poor for all measures.
For this purpose, inter-motif distances were calculated using Smith-Waterman alignment and the Pearson correlation coefficient (R package: MotIV, function: motifDistances) [51].
Fugue does not use predicted secondary structure to determine either the most likely family assignment for a given sequence nor the alignment, and so the correlation gives increased confidence in the fold assignment and alignment.
Metrics such as duplication rate, rRNA abundance, alignment rates, coverage continuity and correlation to reference expression profiles are highly informative during selection of experiment conditions and library construction methods (Levin et al., 2010).
The effect of the following parameters on tree topology comparison was analysed with respect to the different categories: number of sequences per MSA, alignment length, average genetic diversity and correlation of branch lengths.
To determine whether altered structure contributed to a large delta SEN, we examined the delta SEN as a function of base-pair distance between the predicted structure for the subalignment and the given structure of full alignment and found no strong correlation.
The significance of the CAPS correlation values was assessed by randomly pairing sites of the alignment and building a distribution of correlation coefficients for 1,000,000 randomly paired sites against which we compared real correlation values.
