Whether this secondary structure guides G274A editing remains to be determined.
First, since automated methods, like RNASalsa [ 89], remain largely underappreciated, secondary structure guided alignment still relies on extremely time-consuming manual alignment.
Thus, quality assessment of data via e.g. secondary structure guided alignments, discarding of randomly similar aligned positions or heterogeneity of the data set prior to analysis is a crucial step to obtain reliable results.
For all steps fully automated methods were used, including an automated secondary structure guided alignment approach, a software that enables to distinguish random similarity from putative phylogenetic signal, mixed models that avoid artefacts due to co-variation among sites, and analyses that account for variation of evolutionary rates among lineages.
PROMALS3D has advantage over conventional MSA software because it uses structural information and predicted secondary structure to guide the MSA of distantly related homolog.
Ideally, ss-rRNA sequence alignments would use the conserved secondary structure to guide the primary sequence alignment.
For example, the generation of new alignments for each sequence is both computational costly, and does not take advantage of available curated alignments that make use of ss-RNA secondary structure to guide the primary sequence alignment.
In fact, MEMEris 72 uses RNA secondary structure to guide the motif search toward single-stranded regions, and PhyloGibbs 74 integrates conservation information.
In a static homology framework, molecular sequences were aligned using their secondary structure as guide, whereby regions of ambiguous alignment were discarded, and pre-aligned sequences analyzed under parsimony and different mixed models in a Bayesian inference.
Constraint (12) use the secondary structure to guide the sites of the components by allowing insertions if and only if one extremity overlaps or is stacked on top of a base pair.
