The strongest signal of plant promoter is searched with the model of single motif with two types.It turns out that the dominant type is the TATA-box.The other type may be called TATA-less signal,and may be used in gene finders for promoter recognition.While the TATA signals are very close for the monocot and the dicot,their TATA-less signals are significantly different.A general and flexible multi-motif model is also proposed for promoter analysis based on dynamic programming.By extending the Gibbs sampler to the dynamic programming and introducing temperature,an efficient algorithm is developed for searching signals in plant promoters.
Weimou ZhengInstitute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100080, China
In order to show that the newly developed K-string composition distance method, based on counting oligopeptide frequencies, for inferring phylogenetic relations of prokaryotes works equally well without requiring the whole proteome data, we used all ribosomal proteins and the set of aminoacyl tRNA synthetases for each species. The latter group has been known to yield inconsistent trees if used individually. Our trees are obtained without making any sequence alignment. Altogether 16 Archaea, 105 Bacteria and 2 Eucarya are represented on the tree. Most of the lower branchings agree well with the latest, 2003, Outline of the second edition of the Bergeys Manual of Systematic Bacteriology and the trees also suggest some relationships among higher taxa.
WEI Haibin1,2*, QI Ji3,4* & HAO Bailin3,2 1. College of Life Sciences, Zhejiang University, Hangzhou 310027, China
