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The 2D motif is defined as the part of profile which associates tow peaks separated a deep valley (pit).
In case of BsuL-CTD, the metal binding motif is defined by the stretch DQHAAQERIKYEY extending from residues.
A network motif is defined as pattern or architecture of connectivity in gene network that consists of specific regulatory function and recur significantly more often than randomized network [36], [37], [38].
GLAM2 assumes a motif is defined by residue preferences at certain positions called key positions.
For example, position 3 of the LIG_PCNA motif is defined in ELM as [^FHWY].
Each motif is defined by the first occurrence of a repeating nucleotide (eg. GA and AG are unique motifs).
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However, the calculations implicitly assume that the motif was defined before anything was known about the dataset.
The classical CCCH motif was defined as C-X4 15-C-X4 6-C-X3-H [ 6].
The ultraconserved Yfr1 sequence motif was defined as the putative interaction seed.
In brief, an RXLR motif was defined within the first 100 residues.
The resulting output files were computed for the detection of overlapping TR, and the canonical motif was defined using in-home Perl scripts.
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