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GCG substitutes

Jim Phelps phelpsj*stuff* at bcc.orst.edu
Tue Jun 9 17:48:55 EST 1998


In article <8DD3D27DC6A5D111823200A0C955FB4004CBA0 at drucker.niehs.nih.gov>,
staffa at niehs.nih.gov ("Staffa.Nick") wrote:

< snip >
>What DNA and Protein Analysis software are you aware of that would do 
>some of the things that GCG would do and perhaps be friendlier?
>What do you know about it?  How could I find out more?  Would you recommend
>it?

If you are getting sequence data from ABI sequencers, then you should look
at Staden.  It is an X-Windows program that lets you build contigs using
the trace files from the ABI.  It is a bit buggy (under Solaris 2.5.X) but
does some neat tricks, like:

   Click on the contig at a spot where you are wondering (T or G?) and
Staden will open all of the trace files for the sequences that are used to
build the contig.

   It automatically calculates the reverse sequence tracse and inverts the
images (so you work backward along the trace file with the data flipped).

Staden has a web site.  The program comes out of MRC in Cambridge, UK.

I would love to see a summary of all of the replies that you get.

ps.  Let me know if you want me to email you a copy of the help sheet for
running Staden.

pps. Staden may handle other Sequence Data files besides ABI.
-- 
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Jim Phelps                             Computer Support and Planning        
Center for Gene Research and Biotechnology,  Oregon State University
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