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Flow values refer to the signal strength of the sequencing reaction (for details on the sequencing chemistry, see Margulies et al., 2005).
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Edges are drawn depending on the strength of the sequence homology: dotted (BLASTP E value <10−20) or solid (BLASTP E value <10−30).
Systematically higher classification rates indicate that a region showed differential activation patterns for the four sequences, and the size of the classification accuracy served as a measure of the strength of the sequence representation in that region.
The strength of the sequence matches identified and the nearly perfect correlation with HindIII sites used for cloning the BAC library provide strong evidence of the effectiveness of this sequence correlation technique.
Weight of each edge was the strength of the sequence homology relationship as quantified by the pair-wise BLAST E-value – the lower the E-value, the stronger the homology relationship.
Randomizing the 29 positions of the strongest sequence in each DNA fragment abolishes the significant dependence of the original uptake values on the strength of these sequences (e.g., Beta = 0.271, t26 = 1.433 and p-level = 0.164).
The assembled sequences were clustered into 27 groups, based on the strength of these sequence matches across these taxonomic data sets.
We applied a sequence property evaluator that calculates the strength of the SD sequence by searching for a subsequence within the 25 nucleotides upstream of a start codon with highest affinity to the known anti-SD (Lithwick and Margalit, 2003).
Given the strength of the SSOspG sequence in promoting MyoD secretion and activity, we generated additional fusions to this sequence.
In principle, this may be sufficient to infer dependence of the uptake efficiency on the strength of the strongest sequence of a DNA fragment.
Furthermore, it allows the wide analysis of the intergenic regions providing useful information such as the location and strength of the SD sequence.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com