PCgene program

Peter Myler mylerpj at u.washington.edu
Mon Oct 24 11:37:33 EST 1994

On 21 Oct 1994, Hank Seifert wrote:

> > After trying out a few programs for the PC last year, to design PCR 
> > primers, I finally decided to buy PCGENE.  We got the PC version.  We 
> > have been very happy with it.  It is a powerful set of programs.  I don't 
> > know anything about MacVAX.  We had tried Oligo, and we are also using 
> > the GCG program that runs on a VAX.  It's expensive, but worth it.  We 
> > purchased it from IntelliGenetics, which has changeed its name, I 
> > believe.  Anyway, their old  phone was 415.962.7300 in the US.  Is hk 
> > hong kong?  There is a number here for Japan: 81-45-661-3414; and 
> > Belgium: 32-3-219-5354.
> > 
> >
> I've used PCGENE for years and it has its good and bad sides. The programs are 
> well written and can do almost any sequence manipulation and comparison you 
> would want. However, the file orginization capabilities of the program are
> limited. Also, the way files and commands are used in the different program
> modules changes within the different modules. The oneline help is not
> usually very helpful and the manual has little more information. Finally, 
> it is a real problems with loading alternate file types. If you do not mind 
> cursing at the program in a semi-regular time schedule, PCGENE will 
> do the job. 
> We have just ordered GENERUNNER for Windows and are hoping that 
> this program will be easier to useand avoid the switching in and 
> out of PCGENE that we often do now. Does anyone have good or bad 
> experiences with GENERUNNER?
> Hank Seifert
> Northwestern University
I have used GENERUNNER for almost a year now and have found it very 
useful, much easier to use than the DOS based systems.  However, there 
are still sveral things which it still cannot do - sequence assembly 
(coming next year?), sequence alignment (except using MACAW -type 
alignment), and no good graphical outputs.  Still, it is easier to use 
and well worth the investment.  I haven't found any single system which 
will do everything you need for good sequence analysis.  I have to use 
about three or four different programs on two different platforms (PC and 
Unix) on a regular basis.

Peter Myler

Peter J. Myler                                 phone: (206) 284-8846x332
Seattle Biomedical Research Institute          FAX: (206) 284-0313
4 Nickerson Street                             e-mail: MYLERPJ at U.WASHINGTON.EDU
Seattle, WA  98109-1651

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