RBS site?

Anders Gorm Pedersen gorm at cbs.dtu.dk
Fri Nov 10 03:32:55 EST 2000


T V Naga Rama Chander wrote:
> 
> hello,
> is there any website where i'll get collection of sequences that  can
> serve as prokaryotic ribosome binding site?

You may be interested in this graphical representation of the consensus:

   http://www-lmmb.ncifcrf.gov/~toms/gallery/ribo.logo.gif  

The bottom line: the positioning is not completely fixed with respect to
start codon, the sequence itself is not extremely conserved. The most
important part is probably AGGA which is complementary to part of the
16S rRNA.

If you're asking this question in the context of constructing a nice
vector then you should take care also not to have to much secondary
structure near the site. (And of course there are lots of efficient
vectors with RBSes available).

If you want a collection of sequences, then its relatively easy to
extract them from genbank files (one simple solution is to go to the
NCBI genbank site:

  http://www.ncbi.nlm.nih.gov/Genbank/

and simply enter, say, "coli RBS" in the search field.

Best regards,
Anders

--
Anders Gorm Pedersen, Ph.D. (gorm at cbs.dtu.dk)
Technical University of Denmark






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