I used STRAP back in the late 2000s to do structure-based sequence alignments of some TonB Dependent transporters: http://www.bioinformatics.org/strap/
Looks like it is still being updated. Cheers, Jim -------------------------------------------------------------------------- Jim Fairman C: 1-240-479-6575 On Wed, Apr 8, 2020 at 10:22 AM Guillaume Gaullier <guilla...@gaullier.org> wrote: > Hi Armando, > > This seems doable with ChimeraX: https://www.cgl.ucsf.edu/chimerax/ > > More specifically, its matchmaker command will align two structures and > print the corresponding sequence alignment: > https://www.cgl.ucsf.edu/chimerax/docs/user/commands/matchmaker.html > You can then save the sequence alignment to a file, and use it in your > favorite sequence alignment program along with the sequences for which you > don’t have a structure. > > This is one option among many, as pretty much every structure > visualization program can superimpose two similar structures (but I don’t > know how many of them make it as easy to save the sequence alignment). > > Hope this helps, > > Guillaume > > > On 8 Apr 2020, at 19:04, Armando Albert <xalb...@iqfr.csic.es> wrote: > > Dear all, > I want to align two structures and then, I want to align several sequences > to that structural alignment. > How can I do this? > Armando > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
