[ssml] Structure based multiple sequence alignment

rfsouza at cecm.usp.br rfsouza at cecm.usp.br
Tue May 17 15:02:24 EDT 2005


>> 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



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