In addition to the possible problem Ho mentioned (DNA conformational
changes), a few other things could effect how doable it is: percentage
of DNA vs protein in the complex and the resolution of the data.
Too little DNA mass wouldn't help phase the remainder of the complex, if
it could be located.
I suspect everyone is refering to Rost's twilight zone in sequence
similarity where homology modeling trials had better be avoided.
If so, the twilight zone would rather correspond to any indefinite
or transitional condition(s) with no applicable or ever relevant binary
constraint(s).
actually,
Having a generic dictionary definition is nice and dandy. However, in the
present context, the term 'homology' has a much more specific meaning: it
pertains to the having (or not) of a common ancestor. Thus, it is a binary
concept. (*)
But how do we establish phylogeny? - Based on simple
I think we are getting a bit too philosophical on a matter which is
mainly terminology .
1. To quantify how similar two proteins are, one should best refer to
'percent identity'. Thats clear, correct and unambiguous.
2. One can also refer to similarity. In that case it should be
I agree with previous posts that the reality of inferring evolutionary
relationships is often messy, but there is no excuse for being unclear
on the concepts and, in particular, for use of the % homology construct,
still far too common in supposedly good journals.
BTW, %identity is clear but not
But how do we establish phylogeny? - Based on simple similarity!
ah! the old rhetorical trick of changing the problem or question a posteriori!
all i pointed out was that things can't be 25% homologous (well, i can think
of a contrived example in which two four-domain proteins have one
We have used Nanodrop for several years and found the readings are always
accurate. The highest concentration we have measured is around 30 mg/ml. The
differences between diluted and concentrated samples are within dilution
error. Nanodrop spectra at low concentration are noisier. We actually
But how do we establish phylogeny? - Based on simple similarity!
ah! the old rhetorical trick of changing the problem or question a
posteriori! all i pointed out was that things can't be 25% homologous
Well, you were right that in today's definition things can't be. But you
seem to be
- Dima Klenchin [EMAIL PROTECTED] wrote:
But how do we establish phylogeny? - Based on simple similarity!
This is a common, but erroneous, misconception. Modern phylogenetic
methods (Bayesian, maximum likelihood, and some distance-based) rely on
explicit models of molecular evolution, and
- Anastassis Perrakis [EMAIL PROTECTED] wrote:
I think we are getting a bit too philosophical on a matter which is
mainly terminology .
1. To quantify how similar two proteins are, one should best refer to
'percent identity'. Thats clear, correct and unambiguous.
2. One can also
- Dima Klenchin [EMAIL PROTECTED] wrote:
Having a generic dictionary definition is nice and dandy. However, in
the present context, the term 'homology' has a much more specific
meaning: it pertains to the having (or not) of a common ancestor.
Thus, it is a binary concept. (*)
But how
But how do we establish phylogeny? - Based on simple similarity!
(Structural/morphological in early days and largely on sequence
identity today). It's clearly a circular logic:
Hardly. Two sequences can be similar and non-homologous at all levels.
Also, two similar proteins can be homologous
Folks,
This discussion is now dangerously close to a philosophical discourse
regarding the differences between homoplasy, homology, and analogy. Throw
into the mix synapomorphy and symplesiomorphy - and we've got ourselves a
cladistic analysis soup sprinkled with the croutons of phylogeny.
I do
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