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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.

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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.

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  • $\begingroup$ Thanks you for the reply. I just finished reading the documentation. I found out that I can use Chimera to see the percentage of identity, so one problem is solved. The main problem is of a different nature: let's say that I have the MSA from residue 1 to 100 of the query. I would like to have a tool that automatically computes the number of insertions, deletions etc... Some numerical quantities that I can use to see if the alignment is good and how much. Thank you. $\endgroup$ – wrong_path Dec 21 '16 at 16:59
  • $\begingroup$ It would appear that this answer solved the user's question. His comment includes an additional question which is not relevant. I have therefore upvoted it in response to the Cummunity homepage bump. $\endgroup$ – David Apr 20 '17 at 16:58

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