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comparison of sequences from 5'-flanking region - (Mar/13/2006 )

I want to compare 5'-flanking sequences of a particular gene from rat, mouse and human
can u let me know any method to do this
i want to do the comparison to find percentage similarity between both and what sequences are conserved
can u help me get started


are they in the Blast database? I would begin there, for starters


You can use UCSC genome broswer which can show comparative genomics.


Use the emboss programs, look at needle to do pairwise global alignments to get sequence identities and similarity.
To compare all three use emma (also emboss package).