I'm studing the expression of all members of the espansin gene family in grapevine through next generation sequencing technologies.... Given that I found many differences in the pattern of expression of different members in different tissues I'd like to perform a kind of promoter analysis to identyify common and specific cis element which could explain the differential patterns of response... nevertheless I'm not aware of any good database or software which could help me... So far I used PLACE, but I've not idea how good it is and I'd like to use something more sofisticated, or at least something that would allow me to compare the promoter regions of these genes at the same time, not submitting one single sequence for each analysis... I also tryied to use motifLab, that appear to be a very interesting tool, but it requires cis elemts collections to work properly and I can't get these cis collections for plants!
Thanks to all!