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Progressive alignment is further complicated by the potential to introduce errors or bias based on the phylogenetic trees selected for progressive alignment and accumulate pairwise errors at each stage of the alignment [25].
The hh alignment is further manifested through C H···N forces (3.6 Å) between triazole rings of neighboring molecules.
Network alignment is further delineated into two sub-problems: local alignment, to find small conserved motifs across networks, and global alignment, which attempts to find a best mapping between all nodes of the two networks.
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Single and concatenated protein sequences were aligned using MUSCLE [ 73] and each alignment was further optimised using GBlocks [ 74].
The obtained ITS sequences and known sequence of Halophila decipiens Ostenfeld (KC175913) and H. minor (AF366405; AF366406) were aligned by CLUSTAL X [ 42] and the alignment was further modified by eye.
These sequences were aligned by CLUSTAL X (Thompson et al. 1997) and the alignment was further modified by eye.
Primer sequences were deleted and the initial alignment was further modified with GBLOCKS [ 75] to remove ambiguously aligned internal positions and to trim the alignment at the 5' and 3' ends.
Therefore, an iterative in-situ alignment was further implemented into the TIE routine.
The grain alignment was further approved by scanning electron microscopy analysis.
The quality of the target-template alignment was further assessed by comparing the structurally determined (STRIDE) [76] and predicted (PSIPRED) [77], [78], [79] secondary structures.
The alignment was further manually examined and adjusted.
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