How to predict ribosome binding site in Bacteria using PC?

Arnoud van Vliet avvliet at knoware.nl
Sun Jan 31 17:19:38 EST 1999


Dear Yin-suo

don't know about software for that, but in general look for sequences like:

Good RBS's
AGGA
AAGG
AGAGG
AGGG

Weak RBS's
AGGT
AGGC

About 5-25 bp upstream of the ATG / GTG / TTG startcodon. Sorry, you'll
still have to do some visual sequence inspection.

hope this helps
Arnoud

Yinsuo Zhao wrote in message
<3.0.32.19990131215814.006bd644 at public3.bta.net.cn>...
>Hi, Dear friends:
> I've cloned and sequenced a fragment from a kind of Gram-negative
>bacteria. I've analysed its ORF but I can't analysed the ribosome binding
>site  in its promoter. Does anyone know a free or shareware in PC (or any
>internet site) could do this work?
> Thanks for your good suggestion in advance.
>
>Best wishes,
>
>Yin-suo Zhao
>






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