Path: utzoo!utgpu!news-server.csri.toronto.edu!rpi!zaphod.mps.ohio-state.edu!samsung!munnari.oz.au!bruce!lloyd
From: lloyd@bruce.cs.monash.OZ.AU (lloyd allison)
Newsgroups: bionet.molbio.genome-program
Subject: Re: DNA Sequences sought
Message-ID: <3898@bruce.cs.monash.OZ.AU>
Date: 3 Apr 91 00:09:00 GMT
References: <41475@ucbvax.BERKELEY.EDU>
Organization: Monash Uni. Computer Science, Australia
Lines: 71

In <41475@ucbvax.BERKELEY.EDU> tandy@ucbarpa.Berkeley.EDU (Tandy Warnow) writes:
>Sampath Kannan and I have an algorithm which constructs
>phylogenetic trees from DNA sequences for species.  If you
>have aligned sequences, please contact
>     Tandy Warnow

Me too, I'd like the sequences,
but shouldn't someone collect the collections.
A problem like tree reconstruction needs a (large)
set of standard test data.

Lloyd ALLISON
Department of Computer Science, UUCP:lloyd@bruce.cs.monash.edu.au
Monash University, Clayton,     or  :uunet!munnari!bruce.cs.monash.edu.au!lloyd
VICTORIA 3168, AUSTRALIA        Tel :565-5205               FAX: +61 3 565 5146

PS.
1. The beta globin pseudogenes are about 2200 bp
   and form a "close" family often used in reconstructing
   the primate tree:
      ATRB1GLOP, GGBGLOP, HSBGLOP, ORAHBBPS, PTBGLOP

2. J. Jurka has an alignment of many "Alu" sequences, about 280bp each:
   jjurka@net.bio.net
   Family: These are Alu sequences used in study by Jerzy Jurka (Yurek Yurka)
   and Temple Smith, published in Proc. Natl. Acad. Sci. USA
   85: 4775-4778 (1988). The sequences have been aligned by hand 
   using sequence editor - MASE (Faulkner, D.V. and Jurka, J.
   TIBS 13: 321-322, 1988). The enclosed file is in the aligned
   output format useful for 'by eye' analysis. If you need MASE-input 
   ...

3. %A B. F. Koop
   %A M. Goodman
   %A P. Xu
   %A K. Chan
   %A J. L. Slightom
   %A Primate n-globin DNA sequences and man's place among the great apes.
   %J Nature
   %P 234-238
   %V 319
   %D 1986
   %K MolBio, DNA, gene, globin, data, string, psi, eta, globin, pseudo gene
   %X DNA data strings:
       alignment given of human, chimp, gorilla, orang utan,
       rhesus monkey, owl monkey and goat psi-eta globin pseudo 
   ene
   
   %A J. Felsenstein
   %T Evolutionary trees from DNA sequences: a maximum likelihood approach.
   %J J. Mol. Evol.
   %V 17
   %P 368-376
   %D 1981
   %K MolBio phylogentic tree, trees, maximum likelihood, inference
   %X allows for non equal rates of evolution
      DNA data strings: applied to 5 vertebrates' 5S RNA  gives a tree, not seq's
          salmo, chi
   c, family, tree, inductive inference
   
   %A W. Bains
   %T The multiple origins of the human Alu sequences
   %J J. Mol. Evol.
   %V 23
   %P 189-199
   %D 1986
   %K Alu, DNA, Phylogenetic tree, MolBio
   %X uses 62 Alus
      DNA data strings  Blur 1 2 6 7 8 10 11 13 14 19
      Tublin gene beta-5 A to J
      alpha and delta globin locus loci