mapping large segments

[Jared Roach]

In article <v03007800afb3481e7942@[144.92.244.124]>,
Joe Miller <jtmille1 at STUDENTS.WISC.EDU> wrote:
>
>	I am working on a 100kb BAC fragment and have subcloned several
>repetitive and single copy sequences (all less than 3 kb).  I would like to
>make a restriction map of the entire BAC.  Other than subcloning smaller
>fragments (e.g. 10-50 kb) which could take a long time to dissect and order
>does anyone have any suggestions for making a broad baseline map of the
>entire BAC?

	I assume you mean _larger_ fragments?  10 kb subsequences are
one standard for our BAC sequencing group.  You should be able to put 
together a restriction map following multiple complete digest of such 
plasmids.
	An alternative is to end-sequence these plasmids, which offers 
concrete sequence data as well as a map, and may handle repeats better 
than restriction digests.  See for example, my paper: "Pairwise 
End-sequencing.  Roach et al.  Genomics.  26:345-353.  1995."

	I don't know of an "easier" method, barring prior knowledge of 
sequence features of the target, such as STSs or known coding sequences, 
which can be used, for example, to design primers for a PCR based approach.

	Hope this helps.

					-Jared

------------------------------------------------------------------
Jared C. Roach
Department of Molecular Biotechnology
Health Sciences Building, Room K354
University of Washington
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phone  (206) 616-4536
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roach at u.washington.edu
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