[ssml] Structure based multiple sequence alignment

[Dan Bolser]

On Tue, 17 May 2005, Gerard DVD Kleywegt wrote:

>> 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)

I see. Do you use 'environment specific' substitution tables too? (I heard
about these in the context of secondary structure and core vs. surface
'environments').

How much of an improvement in alignments do you get using these
considerations?

Cheers,
Dan. 

>
>--gerard
>
>******************************************************************
>                         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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