conserved amino acid changes

Keith Robison robison1 at husc10.harvard.edu
Tue May 18 17:25:03 EST 1993

David M. Faguy <FAGUYD at QUCDN.QueensU.CA> writes:

>Hello bionetland
>I have a question about conserved amino acid changes. Basically is there
> agreement   on what can be considered   conserved changes? Most papers don't
>define or reference what they call a conserved change. Any reference we can cite
>would be   helpful. Thanks in advance.

I suspect you mean _conservative_ amino acid substitutions.  The conceptual
definition is "a substitution of an amino acid with similar chemical 
properties", such as Ser<->Thr, Asp<->Glu, small aliphatics with
each other, etc.

The best operational definition is amino acids with low substitution penalties
in whatever scoring matrix you are using.  Look up Dayhoff's papers
and Henikoff^2's BLOSUM paper (and others).  For the cites:

	gopher to merlot.welch.jhu.edu
	Menu option: Search Databases at Hopkins...
	Menu option: Seqanalref
	Search terms: amino and substitute

This will get you started -- Seqanalref is wonderful resource for queries
such as this.

Happy hunting!

Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics / HHMI

robison at biosun.harvard.edu 

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