assembly software

Smith Smith
Fri Dec 20 07:55:23 EST 1996


Janet, Young, janet at galton.ucl.ac.uk wrote:
> 
The Staden Package contains a program, gap4 which will do all that you
wish.
It has it's own assembly algorithm and is also capable of interfacing
with both the CAP2 and FAKII assembly programs. Gap4 can read ALF format 
files and has a graphical interface to help you to deal with ambiguities
and conflicts. It is also possible to view the original traces. For
further information, see the web site is at: 

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

Kathryn

> I've been sequencing cDNAs by primer walking using an ALF and an ALF
> express.
> What's the easiest way to assemble the seqeunces and deal with
> ambiguities
> and conflicts?
> 
> At the moment I've just been exporting my sequences in GCG format and
> using the
> GCG fragment assembly software, which is fine until I want to deal with
> the
> ambiguities.  It would be nice to see the traces as I'm doing the
> assembly -
> does anyone know of any software to do this?
> 
> Thanks
> 
> Janet Young
> 
>
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> 
> MRC Human Biochemical Genetics Unit   |   Tel: +44 (0)171 380 7777 ext
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-- 
Dr Kathryn Beal
Structural Studies, Lab Mol Biol, MRC, Hills Rd, Cambridge, CB2 2QH, UK
Phone 01223 402266



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