Exact(17)
Previously, we developed ArcA-binding weight matrices using sequences containing an ArcA binding motif derived from transcriptional profiling and EMSA [13], [26].
Using MPSS, each sample resulted in a library of ∼3,000,000 short signature sequences, containing an average of 290,941 unique sequences (hereafter, simply signatures) with 1,073,382 signatures from all treatments.
However, only 17.8% of the NRSF-bound sequences containing an NRSE (the sequence bound by NRSF) have a window with significant (p≤0.05) overlap between its NRSE its frequent WPH words.
Sequences containing an internal NcoI restriction site (i.e., Pga2) were cloned in two steps.
The sum of the probabilities pi over all the sequences is the expected number of sequences containing an SCD.
In contrast, the discriminating peaks are generated only by those sequences containing an A at the corresponding position.
Similar(42)
Three tandem repeats of partially complementary sequences containing a seed-matched sequence of each of 20 arbitrarily chosen human miRNAs (Figure S1) were introduced into the Renilla luciferase 3′ UTR in the psiCHECK plasmid, hereafter called psiCHECK-SM (Figure 1a).
Following seven rounds of SELEX and sequencing of the affinity-enriched library, we identified a group of related sequences containing a 17 nucleotide pattern that accounted for 18% of the enriched library.
The DNA sequences containing a core motif of SMREs (the red bases).
The same study also showed preferential binding to target sequences containing a mismatch.
A set of 222 non-redundant nucleotide sequences, containing a start and a stop codon, obey the above criteria.
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