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Six different motifs were created with varying levels of specificity in both positioning and sequence (Table 1).
The NMF approach identifies significant matches in both positioning and sequence content for all six inserted motifs in our test set.
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.
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The BLATCAT program can significantly reduce serial steps in comparing specific regions of six representative primate genome sequences and support both position and sequence based approach.
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.
In addition, the transposable elements distributed over the two contigs differ both in their position and sequence.
A set of 875 mapped loci for which both genetic map positions and sequence information were available (Supplementary Table S3) was compared with the genome assemblies of soybean (Glyma1), Medicago (Mt 3.5) and Lotus (Lj 2.5 pseudomolecules) and with the transcript-specific genetic map of cowpea.
Paul devoted my second lesson to training the fingers of my left hand, which were responsible for depressing the strings in the proper positions and sequence.
HSEs evolve in size, position, and sequence within heat-shock promoters.
More suggestions(15)
both conformation and sequence
both size and sequence
both expression and sequence
both error and sequence
both synteny and sequence
both position and sequence
both length and sequence
both timing and sequence
both antigenicity and sequence
both fragmentation and sequence
both positioning and phasing
both positioning and replication
both positioning and content
both positioning and methylation
both positioning and attachment
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