Fitz-Gibbon, S.T., House, C.H.: Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Research 27 (1999) 4218--4222  Home/Search   Document Not in Database   Summary   Related Articles   Check

....inference, the corresponding life forms themselves. Probably the most obvious of such characteristics is the presence absence of representatives of the analyzed species in orthologous groups of genes, and recently, several groups have used this approach to compare the sequenced prokaryotic genomes [4, 14, 17]. The concept and data of clusters of orthologous groups of proteins (COGs) have been developed in [16] see also http: www.ncbi.nlm.nih.gov COG . A COG consists of genes from different species that are genome specific best hits as identified by sequence similarity searches using BLAST. This ....

S. T. Fitz-Gibbon and C. H. House, Whole genome-based phylogenetic analysis of free-living microorganisms, Nucleic Acids Research 21 (1999), 4218--4222.

....In [6] the authors propose to use the order of genes to infer the evolutionary history. This approach does not work for closely related species such as our example where all genes are in the same order in the mitochondrial genomes in all 20 species. Gene Content: Gene content method, proposed in [11, 31], compares number of genes two species share divided by total number of genes. While this approach does not work here due to the fact that all 20 mammalian mitochondrial genomes share exactly the same genes, notice the similarity of gene content formula and our general formula. Rearrangement ....

S.T. Fitz-Gibbon and C.H. House, Whole genome-based phylogenetic analysis of free-living macroorganisms. Nucleic Acids Res. 27(1999), 4218-4222.

....differing evolutionary rates can result in phylogenetic trees with the wrong topology. The recently completed sequences of several organism genomes provide an enormous amount of data with which to address some of these problems. Phylogenetic analysis can also be performed using the whole genome [14, 29], leading to more precise studies. However, only a limited number of genome sequences are available to date, and hence the results of such techniques may not be representative of the whole picture. 2.2 Phylogenetic trees based on metabolic pathways Metabolism is defined as the set of complex ....

S.T. Fitz-Gibbon and C.H. House. Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Research, 27:4218--4222, 1999.

.... the hypothesis of (Rodents, Primates, Ferungulates) The distance matrix can be found at our website (see abstract) The simple asymmetric measure K(xjy) leads to a wrong tree using the same data and programs, as expected (data not shown) The gene order (Boore and Brown, 1998) and gene content (Fitz Gibbon and House, 1999; Snel et al. 1999) approaches, while yielding symmetric distances, have the disadvantage of requiring laborious human analysis of the sequences and also are unlikely to provide enough information to distinguish closely related species such as the above data set. Our method is fully automatic and ....

Fitz-Gibbon, S. T. and House, C. H. (1999). Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res., 27:4218{ 4222.

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Fitz-Gibbon, S.T., House, C.H.: Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Research 27 (1999) 4218--4222

No context found.

S.T. Fitz-Gibbon and C.H. House, Whole genome-based phylogenetic analysis of free-living macroorganisms. Nucleic Acids Res. 27(1999), 4218-4222.

No context found.

S.T. Fitz-Gibbon and C.H. House, Whole genomebased phylogenetic analysis of free-living macroorganisms. Nucleic Acids Res. 27(1999), 4218-4222.

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