phrap .ace file to gap4 database

major major at genome.wi.mit.edu
Fri Dec 7 11:51:58 EST 2001


Thanks James.
I'll poke around the Sanger center and get back ti the group when i get
something working.

John

jkb at mrc-lmb.cam.ac.uk wrote:
> 
> In <3C0BFEDE.F9E45882 at genome.wi.mit.edu> major <major at genome.wi.mit.edu> writes:
> 
> At last - a message that isn't spam!
> 
> > I need to load a phrap ace file directly into a gap4 database, and was
> > wondering if there already exists a tool to do this?  I've looked around
> > in the obvious places, buf have not found anything helpful yet.  Any
> > leads/help is appreciated.
> 
> We don't have any direct ace to gap4 conversion, but we do have patches to
> turn "phrap" into "gcphrap". gcphrap produces experiment files which can be
> imported into gap4 with the Directed Assembly option.
> 
> If you already have existing ace files though then you may wish to check out
> The Sanger Centre's caftools. They swap between a variety of assembly formats
> (but I do not know if this includes ace). I think that both St. Louis GSC and
> the Baylor College of Medicine have conversion tools to go between gap4 and
> consed, but I'm not sure where you'd find them.
> 
> James
> --
> James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Fax: (+44) 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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