contig assembly

Michelle Gleeson Michelle.Gleeson at uts.edu.au
Sun Feb 11 23:40:46 EST 2001


Hi Claudia,

I haven't noticed any "avoid" replies yet, so I thought I'd start.  I 
have extensive experience (or is that extensive frustration?) 
with "AssemblyLIGN", on a Mac platform.  While the partner program 
(MacVector) is OK, the alignment program hasn't been updated much since 
1992/3.  It misses alignments Blind Freddy can see, and is generally 
inconvenient when working on big projects with lots of fragments.  It 
has some nice features, but there has to be something better out there!

Michelle Gleeson
Molecular Parasitology Unit
University of Technology, Sydney AUSTRALIA


----- Original Message -----
From: saharine at cc.helsinki.fi (Juha Saharinen)
Date: Thursday, February 8, 2001 8:18 pm
Subject: Re: contig assembly

> In <cas9-0702011202270001 at vmc3082.vet.cornell.edu> 
> cas9 at cornell.edu (Claudia Sutton) writes:
> 
> >Greetings all... What assembly program are you using? What 
> programs would
> >you avoid, and why?  thanks for any replies.   claudia
> 
> I hav used the Staden package. It is free for academics, and is 
> available 
> for MS Windows and different Unix systems. Its got nice graphics 
> display 
> and the internals are very robust. In my hands, I have been much 
> more pelased with the Staden package than with the commercial 
> conterparts.
> Th url is http://www.mrc-lmb.cam.ac.uk/pubseq/
> 
> Juha
> 
> 
> 



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