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Request for "suggest" functions in gap.

James Bonfield jkb at mrc-lmb.cam.ac.uk
Thu Oct 20 09:31:58 EST 1994

Dear colleagues, our new assembly program (gap) contains
some options to suggest experiments for solving problems
during sequencing projects. This message is a request for
ideas about new options of this type that we could include
in future versions of gap.

Currently gap suggests experiments for filling-in single
stranded regions of contigs and for solving compressions
and stops. Single stranded regions are found automatically
and gap suggests templates that could be used on a "long
gel" machine, or that could be "walked on" using a primer
selected by the program. The compression and stop solving
routine finds "compression" and "stop" tags in contigs and
suggests templates that could be resequenced using Taq
terminators to cure the problem. At present these tags
need to be placed by users from within the contig editor,
but in the longer term we would hope that improved base
calling software might be able to annotate such problems
automatically. However the current semi-automatic method
is still quicker than the user having to select and write
down possible templates to solve problems using Taq 
One idea we have had already is to suggest templates that
could be sequenced using a reverse primer.

So, are there other experimental techniques that people 
would like future versions of gap to help with?

Rodger Staden and James Bonfield
James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 0223 402266   Fax: 0223 412282
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.

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