Briefly, GGP starts with a motif and returns the best fitted motif, according to BIS, by updating each position in m with an IUPAC symbol until no local improvements can be achieved.
To overcome the coarseness of the consensus representation, the best instances of each motif can be extracted from the sequences by using a profile built with the oligos selected by the consensus-based algorithm, in order to have a more fine-grained ranking of predicted motif instances and to detect oligos fitting the motif but exceeding the predefined substitution thresholds used.
Other transcription factors that were identified as fitting the motifs included C/EBPβ, p53, Pax6, Pax2, BCL-6, ATF-5, Kid3 (Zfp354c), and the nuclear receptors SF1, LRH-1, and HNF-4.
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We used ELISPOT assays to test the ability of 15-mer peptides containing sequences that fit the motif to stimulate IFN-γ release by PBMC from these three ECs.
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Finally, we found several sequences fitting an FXF motif (data not shown).
Examination of the human FMRP sequence identified an arginine- and glycine-rich motif fitting this consensus (2, 4).
Some TIRs are located about at the same distance from transposase coding sequences, and are plausibly variants of one or a few sequence types, as they share a motif fitting the consensus GGGGWSAS.
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