Finding ends in phage genomes.
When we repair the terminase gene in SIO1, its ends disappear
and the sequence closes to a circle. A circle is actually what you
expect if you sequence a virus with terminal repeats by shotgun sequencing,
because the assembler will overlap the terminal repeats just like it overlaps
other segments. To find the ends requires some special attention.
The proceedure below is a PCR trick we used to find the VpV262 ends.
It requires some prior guess at where the ends might be in the circle,
which might come from restriction mapping, or be inferred by homology to
another phage, or by having trapped one of the ends directly in a shotgun
clone (as was the case for VpV262).
