Comparing protein families evolution

jungck at BELOIT.EDU jungck at BELOIT.EDU
Tue Apr 18 23:31:50 EST 1995


Dear Dr. Spirov:

Many people have analyzed very different protein families with one another
to look at the rate of replacement of individual amino acids, in what
contexts are amino acids replaced by one another, what is the relationship
between motifs in primary structure with secondary and tertiary structure,
which sequences are more or less susceptible to metabolic degradation and
post-translational modification, etc.  In addition, many investigators have
been interested in questions involving information theoretic and fractal
analyses of sequences in order to understand the efiicency and accuracy of
coding and the potentiality of long range interactions.

I hope that some of these suggestions may be of interest to you.

Sincerely,

John

>          Dear Colleagues:
>     I need ideas and opinions concerning
>following subject. Now we have, in genebanks,
>vast families of diverse genes/proteins.
>As to me, transcription regulators (homeobox,
>Zn-finger proteins, steroid-like receptors etc)
>are the most familiar.
>     My question is: What can we learn (with
>evolutionary point of view) comparing sequence
>changes in phylogenetic tree of one family
>with another? (Say, comparing Antp-like homeobox
>family with Msh or Paired or Engrailed family).
>     All my favorite proteins have super-
>conservative domains participating in DNA and
>peptide recognition and essentially less
>conservative parts.
>     One more question: What software
>could I use for such kind of comparison of
>rates of sequences evolution?
>     Best regards,
>               Alexander Spirov.
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John R. Jungck                                  *
Department of Biology                           *
Beloit College                                  *
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