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Phylogenetic profiling
Phylogenetic profiling is a bioinformatics technique in which the joint presence or joint absence of two traits across large numbers of species is used to infer a meaningful biological connection, such as involvement of two different proteins in the same biological pathway. Along with examination of conserved synteny, conserved operon structure, or "Rosetta Stone" domain fusions, comparing phylogenetic profiles is a designated a "post-homology" technique, in that the computation essential to this method begins after it is determined which proteins are homologous to which. A number of these techniques were developed by David Eisenberg and colleagues; phylogenetic profile comparison was introduced in 1999 by Pellegrini, ''et al.'' 〔Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. Proc Natl Acad Sci U S A. 1999 Apr 13;96(8):4285-8.〕
==Method==
Over 2000 species of Bacteria, Archaea, and Eukaryotes now are represented by complete DNA genome sequences. Typically, each gene in genome encodes a protein that can be assigned to a particular protein family on the basis of homology. For a given protein family, its presence or absence in each genome (in the original formulation) is represented by 1 (present) and 0 (absent). Consequently, the phylogenetic distribution of the protein family can be represented by a long binary number with a digit for each genome; such binary representations readily are compared with each other to look for correlated phylogenetic distributions. The large number of complete genomes makes these profiles rich in information. The advantage of using only complete genomes is that the 0 values, representing the absence of a trait, tend to be reliable.
抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』
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