HomoloGene, a tool of the United States

National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. Th ...

(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. 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 In genetics, the Ka/Ks ratio, also known as ω or ''d''N/''d''S ratio, is used to estimate the balance between neutral mutations, purifying selection and beneficial mutations acting on a set of homologous protein-coding genes. It is calculated as ...

can be calculated. The sequences are matched up by using a

heuristic algorithm In mathematical optimization and computer science, heuristic (from Greek εὑρίσκω "I find, discover") is a technique designed for solving a problem more quickly when classic methods are too slow for finding an approximate solution, or whe ...

for maximizing the score globally, rather than locally, in a bipartite matching (see

complete bipartite graph In the mathematical field of graph theory, a complete bipartite graph or biclique is a special kind of bipartite graph where every vertex of the first set is connected to every vertex of the second set..Electronic edition page 17. Graph theory i ...

). 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.

Input organisms

Metazoa Animals are multicellular, eukaryotic organisms in the biological kingdom Animalia. With few exceptions, animals consume organic material, breathe oxygen, are able to move, can reproduce sexually, and go through an ontogenetic stage in ...

Vertebrates Vertebrates () comprise all animal taxa within the subphylum Vertebrata () (chordates with backbones), including all mammals, birds, reptiles, amphibians, and fish. Vertebrates represent the overwhelming majority of the phylum Chordata, with ...

Homo sapiens Humans (''Homo sapiens'') are the most abundant and widespread species of primate, characterized by bipedalism and exceptional cognitive skills due to a large and complex brain. This has enabled the development of advanced tools, culture ...

, Pan troglodytes,

Mus musculus Mus or MUS may refer to: Abbreviations * MUS, the NATO country code for Mauritius * MUS, the IATA airport code for Minami Torishima Airport * MUS, abbreviation for the Centre for Modern Urban Studies on Campus The Hague, Leiden University, Net ...

Rattus norvegicus ''Rattus'' is a genus of muroid rodents, all typically called rats. However, the term rat can also be applied to rodent species outside of this genus. Species and description The best-known ''Rattus'' species are the black rat (''R. rattus'') ...

Canis lupus familiaris The dog (''Canis familiaris'' or ''Canis lupus familiaris'') is a domesticated descendant of the wolf. Also called the domestic dog, it is derived from the extinct Pleistocene wolf, and the modern wolf is the dog's nearest living relative. D ...

Bos taurus Cattle (''Bos taurus'') are large, domesticated, cloven-hooved, herbivores. They are a prominent modern member of the subfamily Bovinae and the most widespread species of the genus ''Bos''. Adult females are referred to as cows and adult ma ...

Gallus gallus The red junglefowl (''Gallus gallus'') is a tropical bird in the family Phasianidae. It ranges across much of Southeast Asia and parts of South Asia. It was formerly known as the Bankiva or Bankiva Fowl. It is the species that gave rise to the ...

, Xenopus tropicalis,

Danio rerio The zebrafish (''Danio rerio'') is a freshwater fish belonging to the minnow family (Cyprinidae) of the order Cypriniformes. Native to South Asia, it is a popular aquarium fish, frequently sold under the trade name zebra danio (and thus often ca ...

Invertebrates Invertebrates are a paraphyletic group of animals that neither possess nor develop a vertebral column (commonly known as a ''backbone'' or ''spine''), derived from the notochord. This is a grouping including all animals apart from the chordat ...

Drosophila melanogaster ''Drosophila melanogaster'' is a species of fly (the taxonomic order Diptera) in the family Drosophilidae. The species is often referred to as the fruit fly or lesser fruit fly, or less commonly the " vinegar fly" or "pomace fly". Starting with ...

Anopheles gambiae The ''Anopheles gambiae'' complex consists of at least seven morphologically indistinguishable species of mosquitoes in the genus ''Anopheles''. The complex was recognised in the 1960s and includes the most important vectors of malaria in sub- ...

Caenorhabditis elegans ''Caenorhabditis elegans'' () is a free-living transparent nematode about 1 mm in length that lives in temperate soil environments. It is the type species of its genus. The name is a blend of the Greek ''caeno-'' (recent), ''rhabditis'' (r ...

Fungi A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately fr ...

Saccharomyces cerevisiae ''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungus microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have b ...

Schizosaccharomyces pombe ''Schizosaccharomyces pombe'', also called "fission yeast", is a species of yeast used in traditional brewing and as a model organism in molecular and cell biology. It is a unicellular eukaryote, whose cells are rod-shaped. Cells typically measur ...

Kluyveromyces lactis ''Kluyveromyces lactis'' is a '' Kluyveromyces'' yeast commonly used for genetic studies and industrial applications. Its name comes from the ability to assimilate lactose and convert it into lactic acid. ''Kluyveromyces lactis'' (formerly ' ...

Eremothecium gossypii (also known as Ashbya gossypii) is a filamentous fungus or mold closely related to yeast, but growing exclusively in a filamentous way. It was originally isolated from cotton as a pathogen causing stigmatomycosis by Ashby and Nowell in 1926 ...

Magnaporthe grisea ''Magnaporthe grisea'', also known as rice blast fungus, rice rotten neck, rice seedling blight, blast of rice, oval leaf spot of graminea, pitting disease, ryegrass blast, Johnson spot, neck blast, wheat blast, and Imochi ( Japanese:稲熱) is ...

Neurospora crassa ''Neurospora crassa'' is a type of red bread mold of the phylum Ascomycota. The genus name, meaning "nerve spore" in Greek, refers to the characteristic striations on the spores. The first published account of this fungus was from an infestation ...

Plants Plants are predominantly photosynthetic eukaryotes of the kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all current definitions of Plantae exclude ...

Dicots

Arabidopsis thaliana ''Arabidopsis thaliana'', the thale cress, mouse-ear cress or arabidopsis, is a small flowering plant native to Eurasia and Africa. ''A. thaliana'' is considered a weed; it is found along the shoulders of roads and in disturbed land. A winter ...

Monocots Monocotyledons (), commonly referred to as monocots, ( Lilianae '' sensu'' Chase & Reveal) are grass and grass-like flowering plants (angiosperms), the seeds of which typically contain only one embryonic leaf, or cotyledon. They constitute one of ...

Oryza sativa ''Oryza sativa'', commonly known as Asian rice or indica rice, is the plant species most commonly referred to in English as ''rice''. It is the type of farmed rice whose cultivars are most common globally, and was first domesticated in the Yan ...

Protista A protist () is any eukaryotic organism (that is, an organism whose cells contain a cell nucleus) that is not an animal, plant, or fungus. While it is likely that protists share a common ancestor (the last eukaryotic common ancestor), the e ...

Plasmodium falciparum ''Plasmodium falciparum'' is a unicellular protozoan parasite of humans, and the deadliest species of ''Plasmodium'' that causes malaria in humans. The parasite is transmitted through the bite of a female '' Anopheles'' mosquito and causes the ...

''.

Interface

The HomoloGene is linked to all Entrez databases and based on homology and phenotype information of these links: *

Mouse Genome Informatics Mouse Genome Informatics (MGI) is a free, online database and bioinformatics resource hosted by The Jackson Laboratory, with funding by the National Human Genome Research Institute (NHGRI), the National Cancer Institute (NCI), and the Eunice Kenne ...

(MGI), *

Zebrafish Information Network The Zebrafish Information NetworkZFIN is an online biological database of information about the zebrafish (''Danio rerio''). The zebrafish is a widely used model organism for genetic, genomic, and developmental studies, and ZFIN provides an integr ...

(ZFIN), * Saccharomyces Genome Database (SGD), * Clusters of Orthologous Groups (COG), *

FlyBase FlyBase is an online bioinformatics database and the primary repository of genetic and molecular data for the insect family Drosophilidae. For the most extensively studied species and model organism, ''Drosophila melanogaster'', a wide range of d ...

, *

Online Mendelian Inheritance in Man Online Mendelian Inheritance in Man (OMIM) is a continuously updated catalog of human genes and genetic disorders and traits, with a particular focus on the gene-phenotype relationship. , approximately 9,000 of the over 25,000 entries in OMIM ...

(OMIM) As a result, HomoloGene displays information about Genes, Proteins, Phenotypes, and Conserved Domains.

References

External links

HomoloGene
at the

Bioinformatic Harvester
-

Bioinformatic Harvester The Bioinformatic Harvester was a bioinformatic meta search engine created by the European Molecular Biology Laboratory and subsequently hosted and further developed by KIT Karlsruhe Institute of Technology for genes and protein-associated informa ...

, a meta search engine that uses Homologene
OMIMMGIRat Genome DatabaseXenbaseZFINFlyBaseSGDCOG
{{colend Genetics software Bioinformatics