We aim to integrate with more sequence motif analysis tools and web services and to develop further the already included basic protein motif visualization and inference support.
The higher conservation has been attributed to the fact that alternative exons are in general more regulated than constitutive ones, and therefore contain more conserved sequence motifs, like exonic splicing enhancers and silencers, which function in a coordinated fashion.
While the occurrence of TATA-related motifs was established reliably among highly expressed genes, other more prominent sequence motifs distinct from BRE and DPE have been identified in smaller subsets of TATA-less Arabidopsis genes (Figure 1).
The overriding feature of many MAR is that they are AT rich, but several other more specific sequence motifs have also been identified [ 4].
Among PSSM approaches, BioProspector was selected, since, unlike most of PSS algorithms, it features high-order Markov models, which allows one to discover longer and more interspersed sequence motifs [ 31].
Further, instances of positional conservation have been discussed only when 4 or more motifs, and 4 or more sequences with motifs, occurred in a window.
Recent work by Schwartz and colleagues has led to the development of more informative sequence motif representation using Motif-X pLOGos (probability log-based logos) (Schwartz, Chou and Church, unpublished data).
The Motif-directed Profiling approach can be applied to any gene family that has multiple members (at least 30 40), and has one or more conserved sequence motif(s) to allow selective binding of a (degenerate) primer to many gene family members.
High peaks were also generally more associated with sequence motifs (peaks for 5 of 7 TFs in K562 and 7 of 7 TFs in HeLa-S3 were positively correlated with PWM scores).
The APC/C targets proteins for destruction through the recognition of one or more loosely defined sequence motifs in the protein substrate: the destruction (D) box, the KEN box or the Aurora A-like (A) box (Harper et al, 2002; Peters, 2002).
