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Comparative genomic approaches have allowed the identification of conserved occurrences of sequence motifs [6,17].
To identify candidates for direct DNA binding, we searched across the consensus promoters from the cell-specific UniPeak output for occurrences of sequence motifs associated with the TFs in the ENCODE data set.
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Therefore, an imbalance between the proportions of positive serum and the occurrences of sequences should be observed.
Sylamer [9] is another software package that identifies overrepresented occurrences of sequences in a ranked list of genes using the hypergeometric p-value distribution.
The occurrence of sequence and position-dependent HG base pairs provide a new potential mechanism for achieving sequence-dependent DNA transactions.
Our method is based on similarity metrics between two sequences based on the co-occurrence of sequence patterns regardless of their order and orientation, thus tolerating sequence changes observed in non-coding evolution.
This distinction is a further incentive to minimise the occurrence of sequence gaps.
Typically, these methods attempt to extract information from statistical patterns in DNA sequences, e.g., the occurrence of sequence motifs.
The sequencing results were compared with the strain PAO1 sequence (www.pseudomonas.com) with DNASIS Max vesion 2.0 (Hitachi software Engineering), in order to determine the occurrence of sequence variations.
Because the microarray was primarily designed based on the B6 sequence, the occurrence of sequence diversity in probe regions would predict an excess of cisB6 eQTLs.
Within this model, in fact, the probability of occurrence of sequence of words is given as the product of the normalized frequencies of the individual words (see Materials and Methods).
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