Conservation, Evolutionary: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Eran Hodis, Wayne Decatur

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 For example, consider [[1bqh]], which contains 10 chains, representing two copies of a 5-chain molecule. Each molecule contains four sequence different chains. A visit to [http://consurfdb.tau.ac.il ConSurfDB] reveals, not surprisingly, that a different number of sequences was utilized for the multiple sequence alignment (MSA) and conservation calculations for each of these sequence-different chains, and that each MSA had a different average pairwise difference (APD), a measure of diversity within the MSA.
+Therefore, residues with, for example, conservation level 9 (maximal conservation) in each of the three sequence-different chains do not have exactly the same levels of conservation.
+In Proteopedia's ''Evolutionary Conservation'' scenes, we have chosen to color all the chains in the molecule at once. This gives a potentially useful overview, but can be misleading unless one realizes that a given conservation color, in two sequence-different chains, does not mean exactly the same level of conservation. In contrast to Proteopedia's ''Evolutionary Conservation'' scenes,  ConSurfDB and ConSurf Server apply conservation level colors to only one chain sequence at a time, thereby avoiding this possible confusion.
-In Proteopedia's ''Evolutionary Conservation'' scenes, we have chosen to color all the chains in the molecule at once. This gives a potentially useful overview, but can be misleading unless one realizes that a given conservation color, in two sequence-different chains, does not mean exactly the same level of conservation. In contrast to Proteopedia's ''Evolutionary Conservation'' scenes,  ConSurfDB and ConSurf Server apply conservation level colors to only one chain sequence at a time, thereby avoiding this possible confusion.
+A second caveat bears mentioning here. Slight variations in the conservation pattern will occur over time, as the number of sequences in the sequence databases used by ConSurfDB increase. Each update of ConSurfDB uses somewhat larger sequence databases, and consequently, the MSA's for each chain will be slightly different.
 ==The ConSurf Server==