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
t_coffee dataset.fasta -method sap_pair -template_file template_file.template_list
Produces an alignment with an accuracy of usualy higher than 70%- It is possible to combine various structural alignment methods:
t_coffee dataset.fasta -method TMalign_pair sap_pair mustang_pair -template_file template_file.template_list
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