As HEAT repeat sequences are degenerated, many bona fide repeats are not detected by motif detection programs.
Using motif detection programs it is fairly straightforward to identify conserved cis-sequences in promoters of co-regulated genes.
Analysis by motif detection programs indicated that the three TMRs are well conserved compared to the regions exposed to the plastid stroma and thylakoid lumen.
This pipeline integrates three motif-detection programs: AlignAce [ 33], MEME [ 34] and MDscan [ 35].
We use convergent evidence from several transmembrane-prediction and motif-detection programs, including a customised algorithm, LRRscan, to identify eLRR proteins, and a hierarchical clustering method based on TribeMCL to establish their evolutionary relationships.
De novo motif detection using these regions by peak-motif detected ETS⇔CRE motif as the best-enriched motif.
We used the network motif detection tool FANMOD FAst Network MOtiff Detection) 20 for detecting motifs in all networks in Table 1.
The de novo motif detection was performed using a Gibbs sampling algorithm (implemented in INCLUSIVE MotifSampler program [ 17]) in a multi-step procedure.
Consider the experience of BBN's shooter detection program, conceived in a rush four years ago.
This is a clear indication that our surveillance and detection program is working.
