The consideration of sequence surrounding the microRNA binding site on the 3' UTR is sometimes taken into account.
In addition, as shown by our theoretical analysis, consideration of sequencing error can continue to be important even with high-coverage assemblies, particularly for applications in comparative or population genomics.
Nevertheless, these results represent a significant improvement over the prior round of CRM prediction, which used the same search results but without consideration of sequence conservation.
However we show that consideration of sequence divergence is critical for correct prediction in certain cases and can sometimes flag non-cleaved or misannotated targeting signals.
The computer-aided protocol was based on analysis of available crystal structures 1fg9 [ 17] and 1fyh [ 29], consideration of sequence conservation among 32 receptor sequences from 19 species, and free energy calculations by a web-based empirical force field FoldX [ 33].
Consistent with these findings, although we initially found that conserved regions showed low LD levels, after consideration of sequence features one-by-one, we eventually determined that this relationship between LD and conserved regions was distorted by the lack of repetitive elements in such regions.
Consideration of the sequences represented in the flanking sequence of this set of genes revealed it to be diverse; all four nucleotides were represented in 55% of positions and three of the four nucleotides were represented at the remaining positions.
Four attributes are extracted from web page request sequences without consideration of the sequence order of requested pages.
Would consideration of these sequences provide evidence to support, or otherwise, the authors' prediction?
However, further consideration of the sequences suggests an explanation: stabilization of the helical conformation in the RBM by key side chain residue pairs.
