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Zheng Fu wrote:<br>
<blockquote type="cite"
cite="midPine.LNX.4.44.0308081006490.25315-100000@hill.cs.ucr.edu">
<pre wrap="">How to differentiate the fist case(complex cluster) and the
second(distantly related with homolog).
</pre>
</blockquote>
<br>
You have to look at the alignments ... second case would look like...<br>
<br>
<br>
--------------------------A---------------------------------<br>
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||<br>
---------------------------B---------------------------------<br>
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||<br>
----------------------------C--------------------------------<br>
<br>
And first case would be...<br>
<br>
<pre wrap="">A: |------W------/-----X-----|
|||||||||||||
B: |------x-----/-----Y-------|
||||||||||||
C: |------y-------/--------hello mum!------|
</pre>
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<br>
<br>
<blockquote type="cite"
cite="midPine.LNX.4.44.0308081006490.25315-100000@hill.cs.ucr.edu">
<pre wrap="">
And where can I find the information about GENEFAMMER?
</pre>
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<font size="-1" face="verdana,arial,helvetica,sans-serif"> <br>
Bioinformatics 1998 14: 144-150</font><br>
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<br>
<blockquote type="cite"
cite="midPine.LNX.4.44.0308081006490.25315-100000@hill.cs.ucr.edu">
<pre wrap="">
Thank you.
</pre>
</blockquote>
:)<br>
<br>
Dan.<br>
<br>
<br>
<blockquote type="cite"
cite="midPine.LNX.4.44.0308081006490.25315-100000@hill.cs.ucr.edu">
<pre wrap="">
On Thu, 7 Aug 2003, Dan Bolser wrote:
</pre>
<blockquote type="cite">
<pre wrap="">What you describe can occur for 2 good reasons...
You are forming a 'complex cluster', created by *multiple domain*
proteins...
A has domains in common with B,
B has domains in common with C.
A and C have no domains in common, and hence no homology.
I.e.
A: |------W------/-----X-----|
B: |------x-----/-----Y-------|
C: |------y-------/--------hello
mum!------|
OR
A and C are too distantly related for sequence searches to uncover their
true homology. However, sequence B is *intermediate* to A and C,
having homology to both...
B
/ \
/ \
/ \
A C
NB: Sequence similarity is not a metric, as it does not obey triangular
equality.
(I think it is metric at high levels of similarity though?)
In this case you have used the transitive nature of sequence similarity
to uncover
distant homology via an intermediate sequence.
Jong Park and Sarah Techimann worked on both these ideas, and has
created a
family clustering package called GENEFAMMER, Specifically DIVCLUS breaks up
complex clusters into domain families. Transitivity is implemented
(kinda) in psiblast /
hmm models, all three of which are used in PFAM, so you might want to
look there
for your families.
Or you could insist your allignments cover 90% of the shortest sequence,
and then
cluster using single linkage.
Dan.
Zheng Fu wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi everyone,
Does anyone know how to clustering genes to a gene family based on the
sequence alignments.
For two genes, we can define a threshold to seperate the homolog and
non-homolog. But for three or more genes,how to define the homologs?(Such
as Gene A and Gene B has high alignment score, A and C also has high sore,
but B and C doesn't have high socre, can we say ABC are homologs?
Thank you.
Carol
</pre>
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<pre wrap="">
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</pre>
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<pre wrap=""><!---->
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