GAP cannot handle circular sequences. If you want to align
two sequences that you suspect are shifted relative to each other,
you could make a ABCDABCD type repeat of one of them and than
do GAP. This will give you the correct alignment. Other ways to
find out how the sequences are shifted is to do a COMPARE/DOTPLOT
or use the program SIM (enquire huang at cs.mtu.edu). Anyway, to get
a presentable alignment, you will have to edit the sequences with
SEQED and than align them.
Dr. Guy Bottu
