We do not always get information in a well-structured manner, and sometimes we cannot get it in the preferred sequence.
(c) Repeat in numerical (preferred) sequence.
Here, (i) represents a function's position in the preferred sequence, and (F_{j} (x_{j}^ )) represents the optimum of the (j{text{th}}) objective function, found in the (j{text{th}}) iteration (Stadler 1988).
The methods used to characterize the spectrum of mutations in the balanced and unbalanced regions of DNA indicate that MMC interacts with preferred sequences in the DNA, leaving behind an identifiable footprint associated with deletions of variable size.
Moreover, stop codon bias and context also correlates with the efficiency of translation [ 23], so the preferred sequence of translation termination in E. coli, 'TAAT' was used.
More importantly, the preferred sequence of the amino acids differs among the different proteins, as a consequence of the differences in peptide preference.
In addition, the predicted Ets sites at nucleotide positions −216 and −1613 (where numbering is relative to the initiating ATG) of the human MUC4 promoter are almost identical to the preferred Elf5 binding site, with only the 3' nucleotide differing from the predicted Elf5 preferred sequence.
Field et al. [6] found that in over a million of MNase cleavage sites, sequence-specific bias is limited to primarily two consecutive base pairs, and the preferred sequences can be found in nearly all short DNA segments.
Finally, to assess the statistical significance of the observed preferred sequence-distance for correlated mutation positions within helices in the K-domain, we analyzed whether similar preferred sequence-distances occurred within randomly generated stretches of the sequence.
The preferred sequences and locations of βα-hairpin clamps will enhance structure prediction algorithms and provide a strategy for engineering stability in TIM barrel proteins.
DOI: http://dx.doi.org/10.7554/eLife.04251.012 With greater evolutionary distance, differences in the preferred FG sequence context and inter-FG spacer compositions became evident.
