New assembly program

Staden "R." rs at mrc-lmb.cam.ac.uk
Wed May 10 11:02:04 EST 1995

Call for volunteers to assess our new assembly program

At last the gap assembly program has a graphical user 
interface, and although this is important, what really 
counts are the new features a graphical interface has
enabled us to introduce.

The new version has displays of individual contigs to
show their templates, readings, tags and quality plot.
It also has a new type of display that can be used to 
plot possible relationships between contigs, such as
those with common templates, common sequences or weak 
matches between their ends.
Using this information, the relative order of contigs 
can be changed simply by dragging them around on the 
screen. The contig order is stored in the database.
In addition, the new display can be used to activate
the contig joining editor so that possible joins 
between contigs can be examined and made.

With these features we hope that the new  program
will reduce the problems of dealing with repetitive 
sequences and will make it easier to find overlaps 
between contigs.

The new interface is written in Tcl/Tk and has a
consistent Motif style.

We are nearing "completion" of this new version and
are looking for people to try it.

So if you are interested in trying the new program with 
a view to giving constructive comments and bug reports
and influencing its "final" form then please contact 
us directly at staden-package at mrc-lmb.cam.ac.uk

James Bonfield, Kathryn Smith and Rodger Staden

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