Paul Roy proy at rsvs.ulaval.ca
Wed Nov 20 09:18:50 EST 1996

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


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