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automated phylogenomics: Zmasek C.M. and Eddy S.R. (2002) RIO: > Bioinformatics, 3:14. paper available at: http://www.biomedcentral.com/1471-2105/3/14/ Zmasek C.M. and Eddy S.R. (2001) A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics, 17, 821-828 bootstrapping: Algorithms cenancestor: The most recent common ancestor of the taxa under consideration. Walter Fitch “Homology a personal view on some of the problem” Trends in Genetics 16 (5): 227-231 May 2000 Related terms: homology, phylogenomics clade: One of the two kinds of biological entities whose names are governed by this code; a group of species comprising a common ancestor and all of its descendants. PhyloCode Glossary, Ohio Univ. US, 2000 http://www.ohiou.edu/phylocode/glossary.html A monophyletic taxon; a group of organisms which includes the most recent common ancestor of all of its members and all of the descendants of that most recent common ancestor. From the Greek word "klados", meaning branch or twig. [UCMP] Compare species. cladistics: (1) The Journal of the Willi Hennig Society. (2) The scientific discipline of classifying organisms according to the doctrine of Willi Hennig's 1966 book. (3) The belief that the organisation of taxa into groups can only be done by the identification of synapomorphies for that group. [Molecular Systematics] comparative genomics: Functional
genomics evolutionary genomics: The field of plant molecular systematics and phylogeny - using genes to inform taxonomic relationships and evolutionary history ... [aimed at improving our] understanding of how eukaryotic genomes evolve and interact. BA Palevitz, "Evolutionary Genomics: A conversation with pioneer Jeffrey Palmer" The Scientist 14(16): 12, August 21, 2000 http://www.the-scientist.com/yr2000/aug/palevitz_p12_000821.htm Looking at how genes have been preserved through evolution, or how genes or their functions have diverged. evolutionary homology: The methods currently available [1994] for interpreting DNA and protein sequences largely utilize evolutionary homology. The consensus sequence method looks for highly conserved amino acids or bases in specific locations. The weight matrix or profile methods perform the same task quantitatively. Sequence alignments even attempt to recapitulate evolution by specifically postulating substitution, insertion and deletion events that occurred during the evolutionary process. Using these evolutionary based methods, much hypothetical information can be gained from the study of a single gene and protein molecule. However, these evolutionary methods do not give much insight into the flow of genetic information from genes to structure and to phenotype. [Douglas L. Brutlag "Understanding the human genome" in Leder, P., Clayton, D. A. and Rubenstein, E. (Ed.), Scientific American: Introduction to Molecular Medicine (pp. 153-168). New York NY: Scientific American Inc. 1994. http://cmgm.stanford.edu/~brutlag/Abstracts/brutlag94.html Broader term: Functional genomics homology; Related term evolutionary genomics genome prospecting: The 10th annual Genome Issue of Science (October 15, 1999) focuses on "genome prospecting," the use of comparative genome analyses to follow the course of evolutionary history from primordial mammals to humans. Other articles discuss how migration patterns of ancient humans can be reconstructed from traces left in the chromosomal sequences of modern- day descendants, epigenetic mechanisms essential for gene function, improvements in gene expression arrays and their use to categorize human cancers and to support therapeutic decisions, data quality in genomics databases and new bioinformatics directions, and the emerging discipline of pharmacogenomics. Oak Ridge National Lab, US, HGMIS, Oct. 1999 http://www.ornl.gov/hgmis/archive/archives.html homology: Functional genomics Narrower terms: evolutionary homology, positional homology; Proteomics regulatory homology; Sequencing sequence homology; Structural genomics structural homology Related terms: Functional genomics orthology, paralogy, similarity; Structural genomics homology modeling horizontal gene transfer: See xenology; Related term: -Omes & -omics microbiome lateral genomics: It is possible that a single universal phylogenetic tree is not the best way to depict relationships between all living and extinct species. Instead a web- or not - like pattern, reflecting the importance of horizontal or lateral gene transfer between lineages of organisms, might provide a more appropriate visual metaphor. W. Ford Doolittle “Lateral genomics” Trends Millennial Issue (TCB 9(12) TIBS 24 (12) TIG 15 (12): M5-8 December 1999 molecular evolution: Manipulation & Disruption molecular phylogenetics: Attempts to determine the rates and patterns of change occurring in DNA and proteins and to reconstruct the evolutionary history of genes and organisms. Two general approaches may be taken to obtain this information. In the first approach, scientists use DNA to study the evolution of an organism. In the second approach, different organisms are used to study the evolution of DNA. Whatever the approach, the general goal is to infer process from pattern: the processes of organismal evolution deduced from patterns of DNA variation and processes of molecular evolution inferred from the patterns of variations in the DNA itself. Systematics & Molecular Phylogenetics, NCBI, US, 2002, from NCBI's Science Primer http://www.ncbi.nlm.nih.gov/About/primer/phylo.html molecular taxonomy: Relatively new; measure molecular similarity between organisms - related to how close they are related to each other (members of the same species are identical, progressively more distantly related organisms are more and more different at the molecular level). Gordon Curry, Molecular Taxonomy Slide 2 Taxonomy - identifying and classifying organisms , Paleobiology, Earth Sciences Dept., Univ. of Glasgow, Scotland http://www.earthsci.gla.ac.uk/staff/gbc/teaching/Palaeo_Level_3_files/frame.htm See also Cancer genomics monophyletic: A group consisting of an ancestor and all of its descendants; usually used for groups the members of which are more closely related to each other than to any non- members in terms of common ancestry. [PhyloCode] http://www.ohiou.edu/phylocode/glossary.html Related terms clade, species. ortholog (orthologue), orthologous: Functional genomics Narrower term: super- orthologs paralog (paralogue), paralogous: Functional genomics Narrower term: ultra-paralogs phylogenetic: Of or pertaining to the history of ancestry and descent. [PhyloCode Glossary, Ohio Univ. US, 2000] http://www.ohiou.edu/phylocode/glossary.html phylogenetic profiles: Proteins having the same pattern of presence or absence in surveyed genomes ... if there are n fully sequenced genes, there are up to 2n phylogenetic profiles. Currently there are about 30 fully sequenced genomes in the public domain, meaning there are 230 (~10 9 ) possible phylogenetic profiles. This number far exceeds the number of protein families, so that a protein’s phylogenetic profile is a nearly unique characterization of its pattern of distribution among genomes. Hence any two proteins having identical or similar phylogenetic profiles are likely to be engaged in a common pathway or complex. [David Eisenberg et al "Protein function in the post- genomic era" Nature 405: 823- 826, 15 June 2000] Looks at the correlation of protein inheritance across different species. Each protein is given a phylogenetic profile denoting the presence or absence of that protein in various genomes. The result is that function can be assigned to uncharacterized proteins if they have a phylogenetic profile similar to the model profile. [S Spengler “Bioinformatics in the Information Age” Science 287 (5456: 1221-1223, 18 Feb. 2000, citing M. Pellegrini et al. “Assigning protein functions by comparative genome analysis: protein phylogenetic profiles” PNAS 1999 Apr 13, 96(8):4285-8.] Related terms: phylogenetics, phylogenetic tree, phylogenomics phylogenetic shadowing: phylogenetic taxonomy: A system of naming only monophyletic groups of organisms. The hierarchical structure of the names devised by such a system, in principle, accurately reflects the evolutionary relationships of all the named groups of organisms. [Glossary, Natural History Museum, London, UK} http://www.nhm.ac.uk/hosted_sites/pe/2000_1/retinal/gloss.htm Google = about 929 July 19, 2002 phylogenetic tree: A diagram showing evolutionary lineages of organisms. [Edinburgh] In practice, phylogenetic trees are unreliable. Errors in trees will produce spurious inferred duplications. This is obviously problematic if duplications are to be used as indicators of potential functional changes. [Christian M. Zmasek, Sean R. Eddy, RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs, BMC Bioinformatics. 2002; 3 (1): 14, 2002] A graphical depiction of homology. phylogenome: Google = phylogenome = about 9 July 11, 2002; about 9 June 7, 2004, about 19 Aug. 15, 2005, about 20 Oct. 25, 2006 phylogenomic profiling: One of the central goals of bioinformatics is to assign proteins a function from genomic sequences. To this purpose, alignment methods, based on sequence similarity, are still nowadays the most developed and used. Yet, they give indications on the function of only fifty percent of the proteins of an organism. This limit encourages the development of new methods that exploit the information contained within the full sequence of a genome. Those phylogenomic approaches are of course possible because of the recent and massive sequencing of genomes. Phylogenomic profiling is one of the major non- sequence- homology- based method. It is designed to infer a likely functional relationship between proteins. It is based on the assumption that proteins involved in a common metabolic pathway or constituting a multi- molecular complex are likely to evolve in a correlated manner. Phydbac Introduction, Information Génétique & Structurale, C.N.R.S, France http://igs-server.cnrs-mrs.fr/phydbac/introduction.html phylogenomics: Functional prediction via phylogenetic analysis ... When analyzing protein sequences using sequence similarity searches, orthologous sequences (diverged by speciation) are more reliable predictors of a new protein's function than paralogous sequences (diverged by gene duplication), because duplication enables functional diversification. The utility of phylogenetic information in high- throughput genome annotation ("phylogenomics", [1]) is widely recognized, but existing approaches are either manual or indirect (e.g. not based on phylogenetic trees). Here we present a procedure for automated phylogenomics using explicit phylogenetic inference. Christian M. Zmasek, Sean A. Eddy, Washington Univ. School of Medicine; "RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs" Intelligent Systems in Molecular Biology " July 21- 25, 2001, Copenhagen, Denmark poster abstracts] http://ismb01.cbs.dtu.dk/poster_abstracts.html#A35 There are many ways in which evolutionary information can be used to improve functional predictions. Google = about 440 July 11, 2002; about 1,260 July 14, 2004; about 3,050 June 7, 2004; about 14,700 Aug. 15, 2005, about 164,000 Oct. 25, 2006 Related terms: evolutionary genomics, lateral genomics, clades, cladistics, phylogenetic profiles, phylogenetic tree, phylome, subtree- neighbors, super-orthologs, ultra-paralogs phyloinformatics: http://www.phyloinformatics.org/ phylome: The complete set of phylogenetic trees derived from the proteome of an organism. [T Sicheritz- Ponten, SG Andersson, "A phylogenomic approach to microbial evolution" Nucleic Acids Research 15; 29(2): 545- 552 Jan. 2001 Google = about 21 July 11, 2002; about 43 July 14,2003; about 47 June 7, 2004, about 103 Aug. 15, 2005, about 308 Oct. 25, 2006 phyloproteomics: Proteomics positional homology:
Sequence alignment for
phylogenetic analysis has a particular purpose protein subfamilies: Protein structures punctuated equilibrium: A model of evolution in which change occurs in relatively rapid bursts, followed by longer periods of stasis. [UCMP] rooted gene trees: The concept of speciation and duplication is only meaningful on rooted gene trees, but the neighbor joining algorithm infers unrooted trees. We use a simple parsimony criterion for rooting. Gene trees are rooted on each branch, resulting in 2N-3 differently rooted trees for a gene tree of N sequences. For each of these, the number of inferred duplications is determined. [Christian M. Zmasek, Sean R. Eddy, RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs, BMC Bioinformatics. 2002; 3 (1): 14, 2002 species: One of the two kinds of biological entities whose names will eventually be governed by this code; a segment of a population- level lineage that is separate from other such lineage segments as indicated by one or more of various possible criteria (e.g., distinguishability, reproductive isolation, monophyly, etc.). PhyloCode Glossary, Ohio Univ. US http://www.ohiou.edu/phylocode/glossary.html Compare clade. species- nomenclature: Nomenclature subtree: See clade; Narrower term: subtree- neighbors subtree-neighbors: Given a completely binary and rooted gene tree, the k-subtree- neighbors of a sequence q are defined as all sequences derived from the k-level parent node of q, except q itself (the level of q itself is 0, q's parent is 1, and so forth). Subtree- neighbors can be useful if there is (partial) agreement among their annotations ...If the subtree- neighbors lack any agreement in their annotations a useful inference is not possible... Furthermore, orthologs that are not also subtree- neighbors can be misleading. [Christian M. Zmasek, Sean R. Eddy, RIO: , 2002] super-orthologs: Given a rooted gene tree with duplication or speciation assigned to each of its internal nodes, two sequences are super-orthologous if and only if each internal node on their connecting path represents a speciation event. [Christian M. Zmasek, Sean R. Eddy, RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs, BMC Bioinformatics. 2002; 3 (1): 14, 2002] synology: Functional genomics systematics: See under molecular phylogenetics taxonomy: Study of the characterization, classification, and naming of organisms according to standard rules. Most modern taxonomies are phylogenetic (or natural); they attempt to group organisms according to evolutionary descent. [NABIR] This is different from the taxonomies in the Ontologies & Taxonomies glossary ultra-paralogs: Given a rooted gene tree with duplication or speciation assigned to each of its internal nodes, two sequences are ultra- paralogous if and only if the smallest subtree containing them both contains only internal nodes representing duplications [Christian M. Zmasek, Sean R. Eddy, RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs, BMC Bioinformatics. 2002; 3 (1): 14, 2002] xenology: Functional genomics Bibliography |
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it
is the assignment of positional homology. Each column in a
multiple sequence alignment is assumed to include amino acids or
nucleotides that have a common evolutionary history, and each column
is treated separately in the phylogenetic analysis. Therefore, regions
in which the assignment of positional homology is ambiguous should be
excluded (Gatesy et al. 1993).
The exclusion of certain alignment positions (also known as masking)
helps to give phylogenetic methods much of their discriminatory
power. Phylogenetic trees generated without masking (as is done in
many sequence analysis software packages) are less likely to
accurately reflect the evolution of the genes than trees with
masking. Jonathan A. Eisen, Phylogenomics: Improving Functional
Predictions for Uncharacterized Genes by Evolutionary Analysis, Genome
Research 8 (3): 163-167, March 1998