Re: [ccp4bb]: Off topic: structure-based sequence alignments

[Xue-Yuan Pei <xyp20@mole.bio.cam.ac.uk>]

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Dear Dr. Wulf Blankenfeldt:
HUGuE, JOY, Homstrad and Compass will do it for you. You can go to the www
site to find out the detail.

web sites:
http://merlin.bioc.cam.ac.uk/servers.html
http://merlin.bioc.cam.ac.uk/~joy/
http://www-cryst.bioc.cam.ac.uk/~homstrad/
http://www-cryst.bioc.cam.ac.uk/~campass/



Xue-yuan Pei
Department of Biochemistry
Unoversity of Cambridge


On Wed, 31 Oct 2001, Wulf Blankenfeldt wrote:

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>
> Dear all,
>
> sorry for this non-CCP4 question:
>
> We have a bunch of structures that have similar folds but that are not very
> sequence-related (< 20% identity). We would nevertheless like to present a
> multiple sequence alignment based on overlaid secondary structure elements.
>
> Is there a tool that could help us doing this and that has an output format
> readable by other programs, e.g. msf, pir or what have you ??? It should be
> multiple sequences, remember.
>
>
> Thanks for a quick hint,
>
>
>
>
>
> Wulf
>
>
>
> ___________________________
> Dr. Wulf Blankenfeldt
>
> Structural Biology Group
> Biomolecular Sciences Building
> University of St. Andrews
>
> North Haugh
> St. Andrews, Fife
> KY16 9ST
> UK
>
> Tel:    +44 (0) 13 34 - 46 72 82
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> e-mail: wb6@st-andrews.ac.uk
>
>
>