phrap .ace file to gap4 database

jkb at mrc-lmb.cam.ac.uk jkb at mrc-lmb.cam.ac.uk
Fri Dec 7 04:40:00 EST 2001

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 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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