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HomoloGene, a tool of the United States National Center for Biotechnology Information (NCBI), is a system for automated detection of homologs (similarity attributable to descent from a common ancestor) among the annotated genes of several completely sequenced eukaryotic genomes.[1]
The HomoloGene processing consists of the protein analysis from the input organisms. Sequences are compared using blastp, then matched up and put into groups, using a taxonomic tree built from sequence similarity, where closer related organisms are matched up first, and then further organisms are added to the tree. The protein alignments are mapped back to their corresponding DNA sequences, and then distance metrics as molecular distances Jukes and Cantor (1969), Ka/Ks ratio can be calculated.
The sequences are matched up by using a heuristic algorithm for maximizing the score globally, rather than locally, in a bipartite matching (see complete bipartite graph). And then it calculates the statistical significance of each match. Cutoffs are made per position and Ks values are set to prevent false "orthologs" from being grouped together. “Paralogs” are identified by finding sequences that are closer within species than other species.
homologene, this, article, relies, largely, entirely, single, source, relevant, discussion, found, talk, page, please, help, improve, this, article, introducing, citations, additional, sources, find, sources, news, newspapers, books, scholar, jstor, october, 2. This article relies largely or entirely on a single source Relevant discussion may be found on the talk page Please help improve this article by introducing citations to additional sources Find sources HomoloGene news newspapers books scholar JSTOR October 2020 HomoloGene a tool of the United States National Center for Biotechnology Information NCBI is a system for automated detection of homologs similarity attributable to descent from a common ancestor among the annotated genes of several completely sequenced eukaryotic genomes 1 The HomoloGene processing consists of the protein analysis from the input organisms Sequences are compared using blastp then matched up and put into groups using a taxonomic tree built from sequence similarity where closer related organisms are matched up first and then further organisms are added to the tree The protein alignments are mapped back to their corresponding DNA sequences and then distance metrics as molecular distances Jukes and Cantor 1969 Ka Ks ratio can be calculated The sequences are matched up by using a heuristic algorithm for maximizing the score globally rather than locally in a bipartite matching see complete bipartite graph And then it calculates the statistical significance of each match Cutoffs are made per position and Ks values are set to prevent false orthologs from being grouped together Paralogs are identified by finding sequences that are closer within species than other species This resource ceased making updates in 2014 2 Contents 1 Input organisms 1 1 Metazoa 1 1 1 Vertebrates 1 1 2 Invertebrates 1 2 Fungi 1 3 Plants 1 3 1 Dicots 1 3 2 Monocots 1 4 Protista 2 Interface 3 References 4 External linksInput organisms editMetazoa edit Vertebrates edit Homo sapiens Pan troglodytes Mus musculus Rattus norvegicus Canis lupus familiaris Bos taurus Gallus gallus Xenopus tropicalis Danio rerio Invertebrates edit Drosophila melanogaster Anopheles gambiae Caenorhabditis elegans Fungi edit Saccharomyces cerevisiae Schizosaccharomyces pombe Kluyveromyces lactis Eremothecium gossypii Magnaporthe grisea Neurospora crassa Plants edit Dicots edit Arabidopsis thaliana Monocots edit Oryza sativa Protista edit Plasmodium falciparum Interface editThe HomoloGene is linked to all Entrez databases and based on homology and phenotype information of these links Mouse Genome Informatics MGI Zebrafish Information Network ZFIN Saccharomyces Genome Database SGD Clusters of Orthologous Groups COG FlyBase Online Mendelian Inheritance in Man OMIM As a result HomoloGene displays information about Genes Proteins Phenotypes and Conserved Domains References edit Home HomoloGene NCBI www ncbi nlm nih gov National Center for Biotechnology Information Retrieved October 16 2020 Homologene Homologene NCBI Retrieved January 24 2023 External links edit nbsp Wikidata has the property nbsp HomoloGene ID P593 see uses HomoloGene at the National Center for Biotechnology Information Bioinformatic Harvester permanent dead link Bioinformatic Harvester a meta search engine that uses Homologene OMIM MGI Rat Genome Database Xenbase ZFIN FlyBase SGD COG Retrieved from https en wikipedia org w index php title HomoloGene amp oldid 1184338322, wikipedia, wiki, book, books, library,
