NMPDR> FIG Web>Glossary>BidirectionalBestHit  
 

BBH.png
BBH example: the black arrows represent best hits.
The best hit of a particular gene to a target genome is the gene in that genome that represents a best match. The match is bidirectional if the two genes are best hits of each other. A bidirectional best hit represents a very strong similarity between two genes, and is considered evidence that the genes may be orthologs arising from a common ancestor.

More formally, the paper The use of gene clusters to infer functional coupling defines a bidirectional best hit (or BBH) as follows:

Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required SimilarityScores? lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb.

In the SigGenes search, you have the option of using bidirectional best hits or similarities to determine which genes are common among genomes. There are fewer BBHs than similarities, so the BBH analysis is much faster; however, use of similarities produces a more accurate result.

Topic revision: r3 - 09 Apr 2008 - 20:03:08 - BruceParrello
 
NMPDR is a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois. NMPDR is funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract HHSN266200400042C. Banner images are copyright © Dennis Kunkel.