On Wed, 20 Nov 1996, Torben Gjetting wrote:
> Can anyone tell me how to use the gcg package to evaluate possible
> prokaryotic translation starts. Is there an algorithm to score a
> Shine-Dalgarno sequence?
> If an alternative software is available I will be very grateful for
> the information.
There is no GCG implementation of this to my knowledge. "Gene search by
signal" is one of GCG's weak points.
In the old Staden package for VAX (ca. 1984) there was ANALYSEQ which
did score translational initiations using Stormo's W101 matrix. As the
results are qualitative rather than quantitative, it simply drew a
vertical line for hits, but there was no scale. Does anyone know of a
newer implementation of this?
******************************************************************************
Paul H. Roy Phone: +1 418 654 2705
Departement de biochimie,FSG FAX: +1 418 654 2715
Universite Laval E-mail: proy at rsvs.ulaval.ca
Quebec, QC G1K 7P4
CANADA
******************************************************************************
