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However, as it is the case for ARS, the critical ACS motif cannot be predicted only by sequence analysis [31].
Again as in ARS, in NUMTs the key ACS motif cannot be identified just by its level of identity to the consensus sequence or its putative secondary structure stressing the concept that still unidentified sequence parameters contribute to the origin activity and to its efficiency.
This motif cannot be found in the c subunit of T. kivui.
Thus, the found motif cannot be attributed to either of these regulators but only to both of them.
The sub-segment with the highest probability after EM is chosen and modified by iterating the EM algorithm until a candidate motif cannot be improved [ 11].
The disadvantage, however, is that the determination of the "best" motif cannot be guaranteed and is often a very difficult problem since finding global maximum of any continuous non-convex function is a challenging problem.
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If the unit is too small (atomic level), then structural motifs cannot be considered.
Consequently, the function of many motifs cannot be fully determined if the analysis is restricted to discrete instances.
Moreover, the direct-repeat motifs cannot be recognized in most of other gene promoters that bind PhoP.
Surprisingly, most motifs cannot be observed except for five motifs when using the MEME program with the previous reported parameters [ 8, 34].
If the fragments are too small, then the patterns derived from the binding motifs cannot be used, since they are many-body interactions, while using larger fragments limits the application to well-known ligands.
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