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Carlos Frazao wrote:
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Dear ccp4 users
In a molecular replacement case when several homologous 3D exist, is
there an automatic way of aligning the target sequence against the 3D
aligned homologous sequences?
I had a look at clustalx but did not figure out how to align sequence
against a consensual alignment.
Thanks a lot
Carlos
You could try this link:
http://igs-server.cnrs-mrs.fr/Caspr/index.cgi
and use the expert mode.
Or give molrep a try including the line File_S and giving it your
sequence as plain fasta file.
If you still want to try something else, you could visit
http://www.ebi.ac.uk/msd-srv/ssm/
hit the submission key and then the multiple option and keep adding pdb
codes for structure based multiple sequence alignment (of course
uploading your pdb file too).
I personally prefer the last option.
Juergen
--
Jürgen Bosch
Howard Hughes Medical Institute and
University of Washington
Dept. of Biochemistry, K-418
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4542
FAX: +1-206-685-7002
