Sequencher program for ABI373 data

Bruce Roe broe at aardvark.ucs.uoknor.edu
Sat Mar 13 08:01:00 EST 1993


In article <jasons-120393204333 at mac3.medgen.uu.se>, jasons at bmc.uu.se (Jason E Stewart) writes...
>In article <9303081431.AA28019 at geneman.wustl.edu>, rick at GENEMAN.WUSTL.EDU
>> Rick Wilson writes:
>> I can suggest two alternatives:  ted (Gleeson & Hillier, NAR 19, 6481) which
>> runs on Sun SPARCstations and is available free from LaDeana Hillier (lfw@
>> elegans.wustl.edu), and SeqMan from DNAstar which is not free (I don't know
>> how much it costs) and runs on a Mac.  If you want to handle a lot of data
>> and do sequence assembly and editing, I would strongly recommend ted as it
>> has been integrated into the new Staden program xbap.  LaDeana can give you
>> more information about that as well.
>
> Jason Stewart writes:
>The recommendation of the Staden package is useful but only valid if you
>have a connection to a SysAdmin who is going to mount the package on a UNIX
>system and manage it for you, not to mention teach you the necessary X/UNIX
>to be able to access the stuff, not to mention teaching anyone else who
>wants to use the package (assuming that your purchasing this for a
>department and not for solely personal use). This is a large time
>investment. As more biologists take it upon themselves to learn UNIX, this
>will pose less of a problem, but for someone who doesn't know UNIX the
>learning curve for use the Staden package is very VERY low.
> 

	I disagree quite strongly with Jason's comments.  The TED/XBAP package
from Staden, et al. contains EXCELLENT documentation, both on line and
in Mac Microsoft Word format.  It contains binary files on the distribution
tape so all that is needed is for someone to correctly install the programs,
add the path and declare a couple of commands.  The install procedure does
not take a UNIX guru, just someone who knows how to read and type.  As for
the learning curve to use the programs, here there is no real requirement
for much UNIX knowledge since they are X-windows based and it's all point
and click, and if someone takes the time to read the manual, then the learning
curve is dramatically shortenend.

	I agree that dealing with UNIX is a big fat pain in the you-know
what, but if you are doing sequencing on the ABI's and have the money to
buy a Sparcstation, have someone to whom you can turn for some UNIX advice,
and JUST use the Sparcstation for the Staden et al programs, then this very
inexpensive, efficient and useful set of programs is invaluable.  They are
well worth the small amount of time spent learning a little UNIX to get them
operational.  However, there are so very many useful tools for molecular
biology that now are available for UNIX-based computers, that once you have
the Staden et al. programs up and running, you'll be off getting others.

	<stuff deleted>
> 
>Trying to get ABI to make changes is about as teaching a pig to sing so I
>have stopped trying.
> 
	Please don't give up on trying to get ABI to make changes in their
software and hardware.  The more of us that continue to "make suggestion"
to them the more they eventually may listen.  I have the strong tendency
to agree completely with your statement, but it is clear to me that because
they have little competition, the push for improvements MUST come from users.

Cheers.......bruce
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