>> In general how can a single structure be used to improve a multiple >> sequence alignment (if at all)? > > you can align sequences to a structure and have higher penalties for > insertions/deletions in regions of secondary structure (since we know > they are less likely to occur there). this is what we do in Indonesia > (http://xray.bmc.uu.se/dennis) > --gerard Thanks, Gerard! Indonesia is quite what I was looking for. I'll have a look at it! Best regards, Robson