sequence polymorphisms

[Andrew Cockburn]

We have successfully sequenced PCR amplifications of rDNA of individual
mosquitoes (Mol.Bio.Evol. 11:406-416, 1994).  We were sequencing the
ITS2, so one would expect some variation between copies.  In a few 
individuals, there did appear to be polymorphism at certain sites, since
the reads were ambiguous.  In general, however, it worked pretty well.
We think that this is a better approach than sequencing individual clones
of PCR products, since then the presence of PCR artifacts is a real 
problem.

We just starting to sequence some non-transcribed spacers.  With these we
will have no choice but to clone and sequence, since there is lots of
length heterogeneity amongst individual copies.  That will throw the 
different sequences out of phase, which is much worse than ambiguous
reads at a few sites.

Andrew Cockburn
USDA