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HomoloGene[1], a tool of the National Center for Biotechnology Information (NCBI)[2], 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 National Center for Biotechnology Information (NCBI) is part of the US National Library of Medicine (NLM), which is a branch of the US National Institutes of Health. ...
Homology is an important concept in several disciplines: Homology (anthropology) in archaeology and anthropology. ...
The HomoloGene processing consists of the protein analysis from the input organisms. Sequences are compared using blastp[3], 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/Ka ratio can be calculated. A substitution model describes the process from which a sequence of characters of a fixed size from some alphabet changes into another set of traits. ...
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. In computer science, besides the common use as rule of thumb (see heuristic), the term heuristic has two well-defined technical meanings. ...
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. ...
Orthologs are genes in different species which evolved from a common ancestral gene. ...
In biology, two or more structures are said to be homologous if they are alike because of shared ancestry. ...
Input Organisms
Homo sapiens, Mus musculus, Rattus novergegicus, Drosophila melanogaster, Anopheles gambiae, Caenorhabditis elegans, Schzosaccharomyces pombe, Sccharomyces cerevisiae,neurospora crassa, Megnaporthe grisea,Arabidopsis thaliana and Plasmodium falciparum.
Interface The 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.
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