Whereas existing pattern recognition algorithms commonly focus primarily on sequence content, our method simultaneously characterizes both positioning and sequence content of putative motifs.
We have described here a novel approach to the characterization of putative regulatory motifs, using NMF to simultaneously determine both positioning and sequence content.
Analysis of synthetic datasets demonstrates that NMF can accurately describe both positioning and sequence characteristics of implanted patterns, and that NMF finds patterns that are missed by other approaches to pattern recognition.
As with the pan species analysis (Fig. 1d), variability of the aligned species D fiber-knobs (Fig. 2e) confirmed that the β-strands comprising the hydrophobic core of the trimers are highly conserved, with β-strands demonstrating a high degree of overlap in both spatial position and sequence variability (Supplementary Figure 2B).
In addition, the transposable elements distributed over the two contigs differ both in their position and sequence.
We believe that the historical difficulties in clear delineation of these elements are likely due to a convergence of several mitigating factors, including the degenerate sequence content of both the UG- and U-rich elements, significant overlap in both the positioning and sequence content of the two elements, and a typical emphasis on only sequence content in computational investigations.
Zebra finches are able to pay attention to both position and co-occurrence when learning sequences of elements (Chen and ten Cate 2015) and can identify short strings of identical song elements based on differences in element sequence (van Heijningen et al. 2009, 2013; Chen et al. 2014; ten Cate 2014).
HSEs evolve in size, position, and sequence within heat-shock promoters.
