HomoloGene

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

"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]

Input organisms

Metazoa

Vertebrates

"

Danio rerio

"

Invertebrates

"Drosophila melanogaster, Anopheles gambiae, Caenorhabditis elegans"

Fungi

"Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces lactis, Eremothecium gossypii, Magnaporthe grisea, Neurospora crassa"

Plants

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.

References

^ "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

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

[NCBI-1] "Home - HomoloGene - NCBI". www.ncbi.nlm.nih.gov. National Center for Biotechnology Information. Retrieved October 16, 2020.

[2] "Homologene". Homologene. NCBI. Retrieved January 24, 2023.

[1]