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Subsequently, alignment of the assembled contig to the predicted SV region identifies precise SV breakpoints.
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Subsequently, after alignment, each contig is treated as a series of consecutive 200-bp regions.
Subsequently, alignments of INC-regions were examined for secondary folding patterns with LocARNA Ver. 1.5.2 [ 70] and RNAshapes Ver. 2.1.6 [ 71] in order to detect conserved regions.
All of them were first checked by the use of trimAl (automated1 mode) (Capella-Gutierrez et al. 2009); subsequently, alignments were visually inspected: Manual editing was only used to correct few misalignments in proximity of small gaps (supplementary fig. S1, Supplementary Material online).
In the case of SerRS and ThrRS, the respective protein family alignments were subsequently aligned in an additional profile alignment step.
MULTAL deploys a sequential branching method to align the two closest sequences before building up the final alignment by subsequently aligning the next closest sequence to it.
The sequence alignments were subsequently aligned with P. taeda, which was used as an outgroup for each species separately using the profile-profile option in MUSCLE (Edgar 2004).
GSSUs are subsequently aligned and these partial alignments are merged into the final RNA structure alignment and scored.
Subsequently, these alignments were aligned using the profile-profile alignment option in MUSCLE.
Subsequently, multiple alignment analysis was performed with DNAMAN 6.0 software.
Subsequently, the alignment's consensus structure was mapped to that sequence.
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