I am calculating % epitope conservation for different mammalian antibodies against zebrafish. I have performed the Clustal W for antigenic peptide used in raising the antibodies against the respective protein of zebrafish. Can anyone guide me on whether I should consider only the "*" marked amino acids or ":" "." also have to be considered while calculating the % sequence identity.
Awaiting for kind response.
hi,
'*' indicates positions which have a single, fully conserved residue but ':' indicates that one of the following 'strong' groups is fully conserved and '.' indicates that one of the following 'weaker' groups is fully conserved. In an arbitrary look, the first two groups are better.
Hello!
If it is not mandatory for you to use clustal W, you may also try this alignment tool:
http://www.ibi.vu.nl/programs/pralinewww/
I used it several times, it gives information about amino acid conservation level, how many amino acids are identical, etc.
Subhasri Biswas
From my experience, it is recommended to use only "*" marked sequence for better results.
All the best.
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