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GCG substitutes

James Bonfield jkb at mrc-lmb.cam.ac.uk
Wed Jun 10 03:24:41 EST 1998


In article <phelpsj*stuff*-0906981548550001 at phelps-3140-c.cordley.orst.edu> phelpsj*stuff*@bcc.orst.edu (Jim Phelps) writes:
>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:

[cut]

Could you please email any bug reports to staden-package at mrc-lmb.cam.ac.uk.
Suggestions and other comments are also welcome.

As the original poster explicitly requested DNA and Protein Analysis
software I think it's perhaps fair to point out our newer work on this
side. Those who have seen our older programs will know that whilst
very powerful and flexible, they weren't necessarily particularly user
friendly (even the X based ones). We've spent considerable time
improving this interface. For a quick couple of screen shots from the
1997.1 release (1998.0 is the current version, although there's not a
huge deal visually that's changed) see:

	http://www.mrc-lmb.cam.ac.uk/pubseq/screendumps.html

>pps. Staden may handle other Sequence Data files besides ABI.

For trace files we handle ABI, ALF and SCF. For sequence files, we
handle the Staden, EMBL, GenBank, PIR, GCG (perhaps not the very latest
format changes), and FASTA single file formats.

Currently sequence database access is via the original formatted
libraries shipped by the EBI on their own CDs. We do not support the
GCG reformatted libraries, although this will be possible in the next
release as we've now incorporated SRS.

James
--
James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/



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