Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach.
A systematic way of inferring evolutionary relatedness of microbial organisms from the oligopeptide content, i.e., frequency of amino acid K-strings in their complete proteomes, is proposed. The new method circumvents the ambiguity of choosing the genes for phylogenetic reconstruction and avoids the necessity of aligning sequences of essentially different length and gene content. The only "parameter" in the method is the length K of the oligopeptides, which serves to tune the "resolution power" of the method. The topology of the trees converges with K increasing. Applied to a total of 109 organisms, including 16 Archaea, 87 Bacteria, and 6 Eukarya, it yields an unrooted tree that agrees with the biologists' "tree of life" based on SSU rRNA comparison in a majority of basic branchings, and especially, in all lower taxa.
Qi
Ji
J
The Institute of Theoretical Physics, Academia Sinica, Beijing 100080, China, qiji@itp.ac.cn
Wang
Bin
B
Hao
Bai-Iin
BI
D000465:Algorithms; D001105:Archaea / Q000235:genetics*; D001419:Bacteria / Q000235:genetics*; D002965:Classification / Q000379:methods*; D030561:Databases, Nucleic Acid; D009842:Oligopeptides / Q000235:genetics*; D010802:Phylogeny
D009842:Oligopeptides