Although we observed conserved instances of motifs at many different distances, the bin with the highest conservation rate was from 300 400 bp.
This was particularly pronounced when looking at evolutionarily conserved instances (i.e. results from SLiMProb analyses with conservation masking).
Z = x − n p 0 n p 0 (1 − p 0 ) where x is the number of conserved instances of a motif minus the expected number of conserved instances divided by the standard deviation.
We note that though the notion of significance according to our method merely rejects the hypothesis that all the motif instances are unrelated, and a scheme that takes phylogeny into account such as [ 46] may be better suited for this problem in general, our significance evaluation attests to the presence of a highly conserved motif instance in every input sequence.
Removing redundancies: if several relationships are redundant, only the deepest relationship is conserved; for instance, if a HOG 'A' has two substructures by a part_of relationship, 'B' and 'C', and if 'C' is also a substructure of 'B', then the direct relationship between the HOGs 'A' and 'C' is removed.
Based on the distribution of highly conserved predicted motif instances for KstR across the genome, we predict a more general role for KstR in lipid metabolism.
We also analyzed the fraction of these three motifs' instances conserved across the three species, as a function of their distance from the P. yoelii translation start (in bins of 100 bp).
It is fundamentally different from other methods because it is free of the parameters which govern local alignment, thresholding between targets and non-targets, and any distinction between conserved and non-conserved instances of individual binding sites.
Reviewer 3 In discussions of residues differentially conserved within, for instance, the Arf/Arl/SAR group versus the rest of the Ras superfamily it would make discussion clearer to remind readers of this nested superfamily/family structure.
For instance, conserved structural features of molecular determinants on pathogens, termed pathogen-associated molecular patterns, such as lipopolysaccharide (LPS), flagellin, peptidoglycans, microbial DNA and bacterial lipoproteins, are recognized by a set of germline-encoded receptors on host cells, the Toll-like receptor (TLR) family [ 5- 8].
The most conserved intronic motif (GTNAGT, Additional file 1, Table S1), corresponding to a splice donor motif, is both abundant (6648 instances) and well conserved with C.R. (conservation rate) equal to 37%.
