Remember,

To jump to this query's analysis page click on the corresponding link in the navigation bar above underneath the "All Analyses" heading.

Description of the genome query for

Competitive Matching

For each ORF in the chosen genome, or for each ORF in the "Results from my last query,"
a search is made in each target genome from the user's defined set #1 for the best match (and better than the selected threshold) to this ORF. The match score from the very best of these is then compared to the score of the very best of the matches from the target genomes in the user-defined set #2. If the very best match from set #1 is better than the very best match from set #2, the ORF is listed in the output. Sets are defined using the query Define a set of genomes, prior to launching this Competitive Matching analysis.

This query might be useful for finding genes that are more closely related to a member of a distant group, than to any member from a more related group. The user is cautioned to characterize the results further, perhaps by phylogenetic analysis, since many such cases might represent the loss of an orthologous sequence from the more related, set#2, group.

For an example application of this query, please see: Gophna, U., R.L. Charlebois & W.F. Doolittle (2004) Have archaeal genes contributed to bacterial virulence? Trends Microbiol. 12: 213-219.