In article <31191E5B.485E2494 at mackiller.llnl.gov> Chris Barry,
chbarry at mackiller.llnl.gov writes:
>Does anyone have any experience with GCG fragment assemply as compared
>with ABI auto assembler? Any feedback would be appreciated. Thank you in
>advance.
In our institute, we use both of them. The great advantage of ABI
Autoassembler is that it reads the spectras from the automated sequencer
and display sequences with a degenarated IUB cod e (Y for c or t, etc).
We use the server version of this package and the calculations are done
with a sparc server. The great disadvantage is that it makes lot of disk
interrogations and this is very slow on the mac (it doesn't depend from
the calculation mode you use).
Because it displays a consensus, and because the calculation use a
matrix to find the best way to make assembly, it is usefull and sure.
For big projects with lot of "gels", it is really fine. Also, it is easy
to use becaus e of the macintosh interface.
The great advantage of the gcg assembly programms, is that it is (very
!) faster (10 to 100 times !!!), and is free if you already have the gcg
package. There is also very interesting tools in EGCG that allows you to
analyse your project, it is very usefull, if you are doing shotgun
ligations.
In a manager point of view, Autoassembler is heavy for the network
(server version), and not very difficult to install.
So, it is not very easy to say "take this or the other" the answerr
depends from the type of project and the sequencing method, but
Autoassembler is really easy to use, with a good documentation, and need
less organization for the user.
Hope this help
Francois.
Francois Jeanmougin
bioinformatic service
IGBMC Strasbourg France
jeanmougin at igbmc.u-strasbg.fr
