Homologene

Other names: HomoloGene, NCBI HomoloGene

HomoloGene is an automated system for the detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. HomoloGene takes protein sequences from differing species and compares them to one another (using blastp) and matches are placed into groups, using a tree built from sequence similarity to guide the process, where closer related organisms are matched up first, and then further organisms are added as the tree is traversed toward the root. The protein alignments are mapped back to their corresponding DNA sequences, where distance metrics can be calculated (e.g. molecular distance, Ka/Ks ratio). Sequences are matched using synteny when applicable. Remaining sequences are matched up by using an algorithm for maximizing the score globally, rather than locally, in a bipartite matching. Cutoffs on bits per position and Ks values are set to prevent unlikely "orthologs" from being grouped together. These cutoffs are calculated based on the respective score distribution for the given groups of organisms. Paralogs are identified by finding sequences that are closer within species than other species.

Webpage:
http://www.ncbi.nlm.nih.gov/homologene

Licence:
Name: NCBI Data Policies and Disclaimer
URL: http://www.ncbi.nlm.nih.gov/home/about/policies.shtml

Publications:

Tags:

gene genome genome annotation human and other vertebrate genomes model organisms dna amino acid sequence bioinformatics biotechnology chromosome eukaryotic cells genomes homology (biology) mutation phenotype

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