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<P><FONT face=Arial size=2>Hi</FONT></P>
<P>I am currently looking to isolate restriction fragments that cover gaps that
are left in several genomes. To do this I need to cut the sequence we have of a
genome with all known database enzymes and then select those that just cut a few
times and in the right place so as to excise the region of the genome I require.
</P>
<P>GCG programs map and mapplot were excellent for doing this. Map in particular
is good as it gives a graphical plot for each enzyme (one enzyme per line)
plotting all the enzymes on a page or two so you can rapidly see which is
appropriate.</P>
<P>I have tried the EMBOSS programs and basically they are no use. REMAP does
what I want but in too great detail (the output would stretch round the globe)
and RESTRICT is too unordered in its output. </P>
<P>I have got a program called oligo on my PC that will do this, BUT it has
problems with big sequences. Recently I tried analysing a 1.5Mb chromosome and
it would only work if I limited the number of enzymes to 6 or less. So I could
transfer the data over to my PC and try with that but as this organism is 5Mb it
will be very slow going.</P>
<P><FONT face=Arial size=2>Have you any ideas of how this could be done in
EMBOSS.</FONT></P>
<P><FONT face=Arial size=2>M.Quail</FONT></P>
<P><FONT face=Arial size=2></FONT> </P>
<P><FONT face=Arial size=2>Project Leader</FONT></P>
<P><FONT face=Arial size=2>Wellcome Trust Sanger
Institute</FONT></P></DIV></BODY></HTML>