HomoloGene
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Most recent articles on HomoloGene | |
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Ongoing Trials on HomoloGene at Clinical Trials.gov Clinical Trials on HomoloGene at Google
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US National Guidelines Clearinghouse on HomoloGene
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Overview
HomoloGene[2], a tool of the National Center for Biotechnology Information (NCBI)[3], 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[4], 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.
Input Organisms
Homo sapiens, Mus musculus, Danio rerio, Rattus norvegicus, Pan troglodytes, Canis lupus familiaris, Arabidopsis thaliana, Gallus gallus, Oryza sativa, Anopheles gambiae, Drosophila melanogaster, Magnaporthe grisea, Neurospora crassa, Caenorhabditis elegans, Saccharomyces cerevisiae, Kluyveromyces lactis, Eremothecium gossypii, Schizosaccharomyces pombe 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.
External links
- Bioinformatic Harvester is a meta search engine that uses, among others, Homologene: [5]
- NCBI
- OMIM
- ZFIN
- SGD
- COG
- FlyBase
- MGI
- Rat Genome Database
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Acknowledgement and Attribution Regarding Sources of Content
Some of the initial content on this page may be incorporated in part from copyleft sources in the public domain including wikis such as Wikipedia and AskDrWiki. Drug information for patients came from the The National Library of Medicine. Infectious disease information may have come from the Centers for Disease Control (CDC). Differential Diagnoses are drawn from clinicians as well as an amalgamation of 3 sources: 1.The Disease Database; 2. Kahan, Scott, Smith, Ellen G. In A Page: Signs and Symptoms. Malden, Massachusetts: Blackwell Publishing, 2004:3; 3. Sailer, Christian, Wasner, Susanne. Differential Diagnosis Pocket. Hermosa Beach, CA: Borm Bruckmeir Publishing LLC, 2002:7 .
