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Subsequently, every newly predicted sequence has been preliminary aligned to its supposed closest relative using ClustalW, the aligned sequence added to the multiple sequence alignment of the coronins, and the coronin alignment adjusted manually during the subsequent sequence validation process.
Subsequently, every newly predicted sequence has preliminarily been aligned to its supposed closest relative using ClustalW, the aligned sequence added to the multiple sequence alignment of the respective dynactin subunit, and the alignment adjusted manually during the subsequent sequence validation process.
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Once finished, the extended sub-tree is put back to the alignment tree structure, the reference alignment is adjusted for insertions in the new sequences, and the process moves to the next node.
The initial sequence alignment was compared with the initial structure alignment, and adjusted in Jalview to ensure the sequences with unknown structures were properly aligned with the known structures.
In addition, postoperative limb alignment was equal to the left side because alignment was adjusted to the tibial shaft in TAA and TKA.
The alignment was adjusted manually by eye, and ambiguously aligned regions were excluded from the analyses based on similarity criterion [ 92], resulting in a concatenated alignment of 2182 bp.
The initial alignment was adjusted manually and verified using Harmony3 (J. Shi, unpublished), which matches observed substitution frequency in the alignment with predicted substitution frequency from standard and environment specific substitution tables.
The peptide sequences of the domains were aligned with ClustalX (v1.81, with default settings) [ 70] and the alignment was adjusted based on the conserved features of the WRKY domains.
The RvhB7 alignment was adjusted around the conserved lipo-processing site and the "P[ILV]NK" motif [141].
Subsequently, the alignment was adjusted manually.
The generated alignment was adjusted manually.
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