SEQUENCHER FOR UNIX? WHY?

Howard Cash howardc at GENECODES.COM
Wed Oct 2 18:47:25 EST 1996


Don Gilbert posted a query on the AUTOMATED-SEQUENCING group soliciting 
opinions on different software packages for DNA sequencing and assembly.  
He summarized responses on the net at 

   http://www.bio.net/hypermail/AUTOMATED-SEQUENCING/9608/0047.html

There were subsequent postings on the subject 

  http://www.bio.net/hypermail/AUTOMATED-SEQUENCING/9609/0007.html

etc.

> Subject: Summary: Software choice? sequencher, phrap/phred/consed, staden?
> 
> This is a summary of responses to :
> Do you have opinions to share on the best choice(s) of
> software for small-scale autosequencing? ...

[snip snip] 

> My thanks to the many people who wrote me or posted a reply. It is
> good to see so many helpful people sharing their experiences thru
> network news.
> 
> The unanimous favorite software was Sequencher. However only two
> respondents expressed experience with the Unix programs (Phrap &
> Staden),
> so this does not offer as clear an answer as I had hoped. ...

[snip snip...many quoted opinions deleted]

Is there an assumption here that UNIX-based tools have an inherent value 
that is not reflected in an unstructured polling of newsgroup readers?  
Without challenging that premise, what do people think is the main value 
of having sequence assembly software on a UNIX platform?  If Sequencher 
is already such a favorite on the Mac, is there something to be gained by 
going to the trouble to develope a UNIX version?

As an engineer, I like UNIX for software development, but I am biased 
towards the Macintosh for delivering ready-to-use analysis tools.  Larger 
research groups with existing UNIX-based data-management systems ask us 
about porting to that platform, but is there a compelling reason for us 
to develop Sequencher for Unix?  What would the advantage be in the 
average lab, other than the undeniable freedom to work in front of the 
computer of one's choosing?

This should not be construed as a product announcement or a promise to 
port Sequencher to a new operating system, but I would be interested in 
hearing your opinions on the value that you or your immediate colleagues 
would get from a UNIX version. What operating system characteristics 
would you want us to take advantage of that might not be available on a 
Mac.  Keep in mind that, in the real world of finite resources, the 
effort that we would put into porting all or part of Sequencher to a new 
platform would come at the expense of our ability to quickly add features 
to the program if it is only on the Mac.

-----------------------------------------------------------
Howard Cash
President
Gene Codes Corporation

640 Avis Drive, Suite 300, Ann Arbor, MI  48108
Phone 313-769-7249   Fax 313-769-7074
howardc at genecodes.com      http://www.genecodes.com/
-----------------------------------------------------------
Disclaimer:  Although Gene Codes is a commercial software developer, this 
posting should not be construed as an offer to sell software nor to 
develop new programs.  Opinions expressed are my own unless directly 
attributed to others, and do not necessarily reflect those of my 
employer, but - under the circumstances - they often do.




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