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sequence assembler

Mr. D.J. Cain dcain at hgmp.mrc.ac.uk
Thu Sep 9 17:33:37 EST 1999

Dear Sequencers, 

Although I usually have to sit on teh fence as far as newsgroup issues go
I feel so strongly about this issues that I must speak up.  I have been
involved in automated sequencing for over 6 years and have had the
pleasure of working with almost every sequencers that has made it to the
market.  I have also worked with all of the major software packages from
Mac, Windows and Unix as well as a few systems that never reached
commercialisation. I can safely say that Sequencher IS the best package to
perform user level analysis and assembly.  The algorythm is one of the
best I have ever worked with and I have used it for small 2 KB projects as
well as a small genome of 150 KB it more than adequate for most labs.  I
have also taught people to use Sequencher in under 30 minutes regardless
of their previous experience levels.

As a package it is simply feature packed and negates the need to use
multiple programs to analyse different aspects of the sequence.

Cost should not come into the equation of what software you use.  Utalise
the best tools for the job which in my opinion is Sequencher.  If money
matters use the freeware packages but if you want the best dont moan about
the cost, when I buy a car I dont bitch about the premium cars having a
high price becuase I know they are worth it, its the same principle.

I would suggest with anyoen looking at software get demo copies and trial
them.  Find whats best suits your needs and then get it.  If the best
costs more its becuase they invest in the development of the package to
ensure that it grows as our needs as users grow.

I dont want to start a flame war on the subject but having the best tools
will simply enhance your ability to effeciently analyse your data.  


David Cain
( These are of course my own opinions and I would encourage people to
develop their own informed opinions on the matter.  My opinion is also
independant of my newsgroup moderation functions)

On Thu, 9 Sep 1999, John Barlow wrote:

> I beg to differ.  Sequencher is overpriced and has a very confusing interface.  
> Lasergene (www.dnastar.com) is cheaper and more intuitive, however, as it is a 
> Macintosh program recompiled for Windows, it has its share of problems as well. 
>  Nevertheless, it beats Sequencher on price/performance.
> John
> In article <7r6map$s4k at net.bio.net>, jmcconne at clevelandgenomics.com says...
> >
> >
> >
> >> Does anyone know of a PC compatible assembly program that can use ABI
> >> electropherogram files to reassemble the sequences.
> >>
> >Have you looked at Sequencher from Genecodes
> >(http://www.genecodes.com/)?  Their software is very good and they have
> >both Mac and PC versions.
> >
> >
> >Jeff McConnell
> >Director, Genomic Services
> >Cleveland Genomics, Ltd.
> >10515 Carnegie Avenue
> >Cleveland, Ohio 44106
> >
> >tel: (216) 791-5500, out of town call: 1-877-DNA CGCG (1-877-362-2424)
> >fax: (216) 791-5508
> >e-mail: jmcconne at clevelandgenomics.com
> >web: http://www.clevelandgenomics.com
> >
> >
> >
> >
> >Sent via Deja.com http://www.deja.com/
> >Share what you know. Learn what you don't.
> >

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