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
