Conservation, Evolutionary: Difference between revisions
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Eric Martz (talk | contribs) →The ConSurf-DB Mechanism: describing ConSurf-DB Mechanism |
Eric Martz (talk | contribs) →The ConSurf-DB Mechanism: describing ConSurf-DB Mechanism |
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#The filtered sequence set is multiply aligned with [http://www.drive5.com/muscle/ MUSCLE] (a multiple sequence alignment algorithm that out-performs CLUSTALW). | #The filtered sequence set is multiply aligned with [http://www.drive5.com/muscle/ MUSCLE] (a multiple sequence alignment algorithm that out-performs CLUSTALW). | ||
#A phylogenetic tree is constructed from the multiple sequence alignment (MSA) using the Rate4Site program developed by the ConSurf team. | #A phylogenetic tree is constructed from the multiple sequence alignment (MSA) using the Rate4Site program developed by the ConSurf team. | ||
#Rate4Site then calculates an evolutionary rate for each position in the MSA using a [http://en.wikipedia.org/wiki/Bayesian_inference Bayesian] approach shown by the ConSurf team to be superior<ref>PMID: 15201400</ref>. "High evolutionary rate represents a variable position while low rate represents an evolutionarily conserved position."<ref name="consurfdb" /> | #Rate4Site then calculates an evolutionary rate for each position in the MSA using a [http://en.wikipedia.org/wiki/Bayesian_inference Bayesian] approach shown by the ConSurf team to be superior<ref>PMID: 15201400</ref>. "The amino acid evolution is traced using the JTT<ref PMID: 1633570</ref> substitution model. High evolutionary rate represents a variable position while low rate represents an evolutionarily conserved position."<ref name="consurfdb" /> | ||
#"The conservation scores are normalized so that the average over all residues is zero, and the standard deviation is one."<ref name="consurfdb" /> | |||
==The ConSurf Server== | ==The ConSurf Server== | ||
