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An earlier analysis showed that there were differences between published motifs for different ETS-family members, but these differences did not reflect amino-acid features, and might be due to differences in the experimental methods used in different studies (Kielbasa et al, 2005).
Some of these SNPs contain motifs for different TFs.
Figure S3 showed a comparison of found motifs for different methods.
Our approach to identify specific operator motifs for different TF-family members is specific and in essence generic.
Motif databases very often contain multiple motifs for the same TF, or very similar motifs for different TFs.
They compared network motifs for different species and showed that the network motifs are not subject to any particular evolutionary pressure to preserve the corresponding interaction patterns.
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(B ) Box plots indicating half-height widths of ChIP peaks at each individual CTCF motif for different size classes of immunoprecipitated fragments in high-resolution X-ChIP-seq and conventional ChIP.
In order to classify LGI1 into a specific protein domain family, we searched for the presence of sequence motifs characteristic for different families of β-propellers [55].
Some of the peptide residues are buried in the MHC groove and act as anchor residues, which define binding motifs specific for different MHC alleles.
Since the amino acids sequences of AtRecQ4A and OsRecQl4 are quite similar to each other, and differ slightly from that of AtRecQ4B protein, we hypothesized that AtRecQ4B protein has acquired or lost specific motifs required for different functions.
Four Zur-binding motifs described for different proteobacteria [08, 22, 32, 33] were aligned in order to identify conserved sequences, which were in turn used to perform a genome-scale screening for putative Zur-binding sites in the C. crescentus genome sequence in the RSAT website [ 53].
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