How does Belvu calculate conservation scores?

Question

[jmungar2]

I am using Belvu to calculate per-residue conservation scores but I could not find either in the manual nor in the SeqTools paper how conservation is calculated (Shannon entropies, similarity, etc).

For example, Belvu gives me sometimes low conservation values (2-3) for high values of percentage identity (over 80%), or give me a value of 4 for 100% sequence identity. Any idea of where can I find this information?

Thank you

[Mensur Dlakic]

I don't know the exact answer, but from what you wrote my guess is that the conservation is based on information content. You can read more about that by Googling sequence logo. The maximum information content for proteins is log[2] (20) = 4.321928095, where 20 is the number of amino-acids. For nucleotides it would be log[2] (4) = 2.

[jmungar2]

Thank you for your response. Actually, I also get values way over 4.3, up to 11, so it's a bit confusing...