Predicting transcriptional terminators in bacteria

C. J. Fields cjfields at jove.acs.unt.edu
Wed Mar 7 12:18:33 EST 2001


TIGR has a program to do this (TransTerm), but it requires UNIX and is not
a web server (see http://www.tigr.org/softlab/transterm.html).  The
Pseudomonas genome server in Australia has used this program for finding
terminators in the PAO1 genome sequence.

Rho-ind. terminators are easy enough to find (string of T's in DNA or U's
in RNA, preceeded by G-C rich region which has secondary structure).  I
think there was a method to look for rho-dep. terminators dependent on the
ratio of C's present in the sequence and the presence of rut sites in the
sequence.  A region rich in C's over G's (a C>G "bubble") preceeded
rho-dep. termination.

Both of the previous can be found by a search of PubMed (terminators and
motifs, maybe?)

CJ Fields

Alejandro Miguel Martin Dunn wrote:

> hi everybody,
>
> Are there any public servers out there doing prediction of prokaryotic
> transcriptional terminators, rho-independent or otherwise? I've done
> some searching but have come up empty-handed so far.
>
> cheers,
> alejandro
>
> ---------------------------------------------
> Alejandro Martin
> Centro de Ingenieria Genetica y Biotecnologia
> PO Box 6162, C. Postal 10600
> Ciudad Habana, CUBA
> Tel: (53-7)216221, FAX: (53-7)214764
>
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