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

[Patrice GOUET <p.gouet@ibcp.fr>]

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Hi Wulf,

> We would nevertheless like to present a
> multiple sequence alignment based on overlaid secondary structure elements.

A new option has been added in ENDscript
(http://genopole.toulouse.inra.fr/ESPript/cgi-bin/nph-ENDscript_exe.cgi)
to display in one go all known 3D structures in a sequence alignment.
This option is being tested and should be implemented to the cousin web
server ESPript next week.

> We have a bunch of structures that have similar folds but that are not very
> sequence-related (< 20% identity).

You will also find in ENDscript, an example on how to align distant
sequences with similar 3D structures. We are using TOP
(http://bioinfo1.mbfys.lu.se/TOP/)
to superimpose structures and the sequence editor SEAVIEW
(http://pbil.univ-lyon1.fr/software/seaview.html) to correct the multiple
alignment.
cheers
patrice