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Contig assembly?

Richard Durbin rd at mrc-lmb.cam.ac.uk
Wed Jun 15 17:17:18 EST 1994

eesnyder at sequana.com asks about contig assembly in ACEDB.

Unfortunately this has a messy history.  The physical map display was
based on the program CONTIG9 written by John Sulston for the C.
elegans mapping project.  Contig9 had full editing and fingerprint
based assembly functions, but the acedb pmap display was originally
only for display of a current state of the map.  We intended to bring
all the editing functions across into acedb, but the person assigned
to do the task turned out to never complete it, and eventually left,
leaving a nearly working mess that nobody else wants to look at.  This
is the code reffered to in the help pages, which is not linked into
the release, so you won't find it.  Sorry for not removing the
references in the help pages.

Since then we have in fact completed a Unix/X port of the original
contig9 software, but outside ACEDB.  In fact this was based on an
automated f2c translation of the VAX fortran, with ACEDB/X graphics
replacing all the terminal based graphics.  This program is called
contigc, and is either now or very soon will be available from
Friedemann Wobus (fw at sanger.ac.uk).  Since the "look and feel" is
still that of a textronix terminal system there is essentially no use
of the mouse, and it looks old-fashioned, but seems to work exactly as
the VAX code did.

More relevant to ACEDB, Jean Thierry-Mieg and Ulrich Sauvage have been
working on new physical map assembly functions linked into the modern
vertical map display of ACEDB.  I gather they have some impressive
results and the interface is more intuitive and potentially much more
powerful.  I suggest you contact them (mieg at crbm.cnrs-mop.fr or
ulrich at crbm.cnrs-mop.fr) to find out the current state of their
system, and whether they can support an active mapping project.

Richard Durbin

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