| AAPPS Bulletin
Vol. 16 No. 3,
June 2006 |
Highlight of the Issue
Simple Markov Subtraction Essentially Improves Prokaryote
Phylogeny (PDF,
745KB)
Lei Gao†,
Ji Qi‡, and Bailin Hao†
†
Institute of Theoretical
Physics, Academia Sinica, Beijing, China
‡
Center for Comparative Genomics and
Bioinformatics, Penn State University, USA
Abstract
This is a brief review of a new method for reconstructing
evolutionary relationship of bacteria from their complete
genomes. Significant improvement has been achieved by making a
simple Markov assumption to subtract a "random" background from
the counting results of short peptides in the collection of
protein sequences of a species. The
phylogenetic tree obtained in this way may be compared in
details with the latest taxonomy as reflected in the Bergey's
Manual of Systematic Bacteriology. |
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