Getting the best out of T-Coffee

  • Default Expresso
      The expresso mode will run a blast between your sequences and the EBI, identify the best templates, download the PDB files and use them. The templates are reported in the file template_file.template_list. The templates may vary because they depend on the version of the PDB. If you want, you can produce this file yourself, or re-use a previous one.
  • Customizing Expresso
    1. t_coffee dataset.fasta -method sap_pair -template_file template_file.template_list
      Produces an alignment with an accuracy of usualy higher than 70%
    2. It is possible to combine various structural alignment methods:
    3. t_coffee dataset.fasta -method TMalign_pair sap_pair mustang_pair -template_file template_file.template_list
  • Questions should be sent to C.Notredame