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Partial vs. whole trees

guest at informatics.lan.nrc.ca guest at informatics.lan.nrc.ca
Fri Mar 19 15:19:18 EST 1993

In article <MAILQUEUE-101.930316102321.158 at micro.uct.ac.za> ED at micro.uct.ac.za ("Ed Rybicki") writes:
>From: ED at micro.uct.ac.za ("Ed Rybicki")
>Subject: re: Partial vs. whole trees
>Date: 16 Mar 93 09:38:41 GMT

>> In article <9303121847.AA05027 at net.bio.net>, preissj at CLVAX1.CL.MSU.EDU ("J Preiss--Seq Anal") writes:
>> >
>> I just thought it might be worth pointing out that one can hardly grow a
>> tree as suggested above when there is a single taxon whose complete genome
>> has been sequenced.  The essence of tree building is comparing homologous
>> sequences from a variety of taxa.  So perhaps the question should be:
>> has anyone tried building a tree of several genome sequences (or several
>> sub-genomic sequences) from taxa whose genomic sequences can be align
>> ed with confidence.

>Yes - again, with viruses, as these are the only organisms whose genomes
>are small enough that sufficient have been sequenced to give any sort of
>approach to treeing.  For example, there are now a large of number of
>complete sequences for picornaviruses, retroviruses, influenza and
>paramyxo- and rhabdo- and poty- and geminiviruses, and an even larger
>number of partial sequences from relatives of all the above.  I have
>played with gemini-, poty- and picornaviruses, and my conclusions are that
>using a conserved predicted partial polypeptide sequence from any of these
>is sufficient to give the same tree (give or take a branch) as you get
>from the entire sequence.  You may argue that virus genomes are so much
>smaller than those of cellular organisms that any conclusions reached from
>study of whole vs. partial sequences for viruses have no relevance to the
>larger beasties - but would you be right?  Viruses represent the limit of
>the problem in that they do not normally have any "wasted" sequences
>because of informational constriants on small genomes; however, the
>largest viruses have the same size genomes as the smallest cells (eg.
>poxviruses vs. mycoplasmas), and the entire genomes of several
>herpesviruses and poxviruses have already been determined (+/-200 kb each)
>- so there is material to test the odd hypothesis.

>  ____________________________________________________________________
> | Ed Rybicki, PhD             |     "Emancipate yourselves from      |
> | (ed at micro.uct.ac.za)        |            mental slavery            |
> | Dept Microbiology           |          None but ourselves          |
> | University of Cape Town     |         Can free our minds...."      |
> | Private Bag, Rondebosch     |                                      |
> | 7700, South Africa          |             - Bob Marley             |
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