I have to do homology modeling for a transmembrane protein (sodium channel) and right now I am in the process of aligning the sequences of the template with the homologous proteins I have found. I am using T-Coffee to do the alignment. I would like to have some numerical descriptors of the different sequences and I have been told to include the percentage of similarity and identity. How can I compute them? Is there an on-line tools to do this? Thank you.
I've never used T-Coffee but it looks like the web-server version gives you a total score as well as a score for each individual sequence; do you know if those numbers are related to the numerical descriptors you need? A good place to start would be to read the documentation. Another good place to look would be the Google Groups page for T-Coffee.