DNA data for humans, apes and outgroup?

Laurent Duret duret at acnuc.univ-lyon1.fr
Fri Aug 11 04:55:50 EST 1995


Ludvig Mortberg (Agneta.Guillemot at historia.umu.se) wrote:
: Does anybody know how much DNA or proteins have been sequenced in the
: apes and outgroups for cladistic analysis? I'm not interested in the
: actual sequences of course. Just knowing which proteins or sequences
: would help when I search abstracts for articles on the actual
: sequences.

This is what HOVERGEN database is made for. HOVERGEN (Homologous Vertebrate Genes
database) contains all vertebrate sequences from GenBank, classified into families
of homologous genes. Protein multiple alignments and phylogenetic trees have been
calculated for each family and can be visualised on a graphical interface. Have a 
look at:

http://biom1.univ-lyon1.fr:8080/www/doclogi/hoverangl/ahoverdoc.html

to see what this interface looks like, and 

http://biom1.univ-lyon1.fr:8080/www/doclogi/hoverangl/ahovergen.html

for more general information.

HOVERGEN data and softwares are freely available through anonymous ftp at 
biom3.univ-lyon1.fr    or    134.214.92.37
in the directory /pub/hovergen

HOVERGEN has been described in:

L. Duret, D. Mouchiroud & M. Gouy (1994) HOVERGEN: a Database of 
Homologous Vertebrate Genes. Nucleic Acids Research 22:2360-2365



I quickly searched in HOVERGEN for genes known in chimp, gorilla, orang, homo and a
non hominidae primate as outgroup. I found 10 such genes (besides the ones you 
already have):

protamine 1
involucrin
PrP prion-protein
complement component C4A
eosinophil cationic protein ECP
SRY
immunoglobulin
MHC class I
mitochondrial cytochrome c oxydase COX-2
mitochondrial protein A6L / ATPase subunit 8

Some of these genes are probably useless for phylogenetic studies (immunoglobulin, 
...), and you will also have to check for paralogy.


Hope this helps,

Laurent Duret


================================================================
Laurent Duret			    duret at biomserv.univ-lyon1.fr
Tel: 	+33 72.44.81.42		    Fax:	+33 78.89.27.19
Laboratoire de Biometrie, Genetique et Biologie des Populations
Bat 741 - URA CNRS 243 Universite Claude Bernard - Lyon I
43, Bd du 11 Novembre 1918 
69622 Villeurbanne cedex FRANCE
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