[ssml] Structure based multiple sequence alignment

[Gerard DVD Kleywegt]

> 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

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                         Gerard J.  Kleywegt
     [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                 Biomedical Centre  Box 596
                 SE-751 24 Uppsala  SWEDEN

     http://xray.bmc.uu.se/gerard/  mailto:gerard at xray.bmc.uu.se
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