utilizing restriction maps in sequence assembly?

Jonathan Epstein Jonathan_Epstein at nih.gov
Fri May 14 08:32:13 EST 1999


Hi,

I'm trying to help a group here which is having a BAC sequenced.

The people who are doing the sequencing report that the Phred/Phrap
assembly fails due to lack of sufficient coverage (4x) and a large
number of repetitive elements in the sequence.  Apparently there are ~50
resulting contigs.

It turns out that the group which I'm helping has performed digestions
using 4 different 6-base restriction enzymes, and has tabulated this
data.

It seems intuitively that this restriction enzyme data could help in the
assembly, i.e., one could correlate electronic digestion of the contigs
with the known restriction enzyme patterns.

Does anyone have any suggestions regarding software which can assist in
this task?

TIA,

- Jonathan




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