STADEN Package and sequencer data analysis

Bruce Roe BROE at AARDVARK.UCS.UOKNOR.EDU
Fri Nov 1 07:19:00 EST 1991


Mike Smith writes: 
=>  
=>        We have a automated sequencer and a Sun workstation.  Through the 
=>   grapevine the STADEN package has been suggested as a potential solution
=>   to analyzing our .alf files and analyzing multiple runs over the same
=>   region of DNA.   So I have several questions for the net.
=>   
=>   1) Is anyone else using a sun to analyze data from either the Pharmacia
=>   or Applied Biosystems Sequencers?  And what software do you use??

	We are using the XDAP and TED programs described in:
	Dear, S. and Staden, R. Nucl. Acids Res.  19, 3907-3911 (1991).

=>   
=>   2) Where can I get a copy of the Staden package?? 

	You can get a tape with source and SPARCstation executables from
	Rodger Staden at:
		MRC-Lab. Molecular Biology
		Hills Road
		Cambridge, England  
	Staden's e-mail address is:
	RS at mrc-molecular-biology.cambridge.ac.uk

=>   And will this software do the job?

	This depends on what "job" you want them to do!
	We use the TED program for proofreading before gel assembly and
	XDAP for gel assembly, and don't know of any other programs which
	are as worthwhile for these processes.  Plus they are rather
	inexpensive and very well done.  I recommend them highly.

=>   
=>   Thanks in advance.
=>   
=>   mike 
=>   
=>     *********************** Michael W. Smith **************************
=>     *             Salk Institute for Biological Studies               *
=>     * Molecular Genetics Laboratory     phone: (619)453-4100, ext 376 *
=>     * P. O. Box  85800                  fax:   (619)558-9513    or 536*
=>     * San Diego, CA   92138             E-mail: mws at molly.sdsc.edu    *
=>     *******************************************************************
=> 
	Hope this helps...............bruce
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