Plasmid construction simulation.

Peter Gegenheimer peterg at rnaworld.bio.ukans.edu
Wed Apr 20 17:58:20 EST 1994


In <9404161824.AA28195 at alliant.snu.ac.kr>, hosun at ALLIANT.SNU.AC.KR writes:
>Hello, Netters.
>
>Is there any one heard of the program manuplate plasmid sequence?
>
>I want to make a program simulate plasmid manuplation. 
>display restriction fragments and plasmid map.
>make result plasmid sequence. and so on..
>
>like Restriction with EcoRI and elute small fragmet.
>     and then Blunting with Klenow fragment of DNA Pol.
>     and ligating with SmaI digested vector.
>then what result is expected?
>Is this stratagy valid?

The program you want -- for the IBM PC -- is CLONE 4 (CLONER) from Scientific & 
Educational Software, P.O. Box 440, State Line, PA 17263, USA. Phone 
717-597-5307. This is a VERY well-designed program that does everything you 
want. Single or multiple enzyme digests, select fragment of interest, fill-in or
chew back ends if needed, ligate with another fragment. Not only is the DNA 
sequence carried along, but the map locations of genes and other features, and 
restriction sites, are recalculated. You can then rescan open reading frames to
see whether you've made an in-frame ligation, etc. Restriction mapping is 
flexible and powerful. Circular maps can be drawn; a separate 
program is available to make publication-quality maps. Reads a number of 
sequence file formats; from Genbank and EMBL files the locations of coding 
sequences are automatically extracted and displayed on the map.

I've been using their Cloner, Primer Designer, Sequence alignment, and 
graphics programs for years. The program designer is a former lambda phage 
researcher who is an EXCELLENT programmer. Demo disks are available.

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|  Peter Gegenheimer                          |  pgegen at kuhub.cc.ukans.edu      |
|  Departments of Biochemistry and of Botany  |  voice: 913-864-3939            |
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