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Search homologus sequences - (Nov/17/2009 )

Hi Everyone..!
I want to search whether a particular inverted repeat sequence present in the promoter region of E.coli gene is also present in other species of bacteria. Since it is just a 20bp long region, I dont know how to use NCBI blast option :( guide me pls :) . I thank all of you..



I think BLAST will be your best bet, just filter for the bacteria you'd like to test and be prepared for lots of hits to sift through. especially things like regulatory promoter sequences, which are insanely redundant.

I don't think there's actually going to be an easy way to do this :wacko:

there are also promoter analysis softwares available which can calculate probabilities about your sequence being involved with the promoter based on neighboring sequences...? is that what you're looking for?