> I want to do the sequence alignment of these two proteins from all > species in such a way that the structure based sequence remain constant > while extending the sequence only at the c-terminus.
IIUC : profile 1 = *structure-based* sequence alignment i.e. from STAMP (THESEUS?) profile 2 = a huge sequence alignment i.e. from MAFFT or CLUSTALW2 with both *profiles* in hand, these comes to mind : [1] clustalx : load profile 1. choose "profile mode" (?) then add profile 2 to it [2] Jalview : load profile 1. then add profile 2 to it [3] mafft : command line : mafft-profile profile_1.aln profile_2.aln > all.aln there's pulldowns in [1,2] that will lead the way. i can say [1,2] work in my hands to align sequences, and then browse through them or print them. haven't tried [3] for structure-based profile alignment. ... BTW, if anyone wants a molecular replacement search probe, this is very interesting : phenix.sculptor a_structure.pdb huge_sequence_alignment.[ali,fasta,..] BTW they are helpful over on the Jalview discussion group : http://www.jalview.org/mailman/listinfo/jalview-discuss HTH -Bryan
