Description of the genome query for

ORFs shared exclusively with one or more lineages

For each ORF in the chosen genome(s) or for each ORF in the user's "Results from my last query" , it is determined if the ORF matches database entries in exactly the chosen number of lineages (within the chosen taxonomic level) at better than the chosen inclusion cutoff, but in no other lineage (within the chosen taxonomic level) at better than the chosen exclusion cutoff.

If "Exclude ORFs which match other lineages above chosen taxonomic level" was selected, it is determined if the ORF matches database entries (at better than the exclusion cutoff) in any non-self lineage one up from the chosen taxonomic level.

An ORF is reported if it passes all of the above tests.

Examples:

Suppose that we are interested in finding ORFs from Haemophilus influenzae, a gamma proteobacterium, that match only one of the other subdivisions of Proteobacteria, i.e., alpha, beta, delta or epsilon. This could be due to a variety of reasons, including rapid evolution (the ORF is found only in the sister group to gamma), or the selective loss or gain of ORFs. In order to be certain that an ORF is present in one lineage, and that it is not present in the others, we choose a reasonably stringent inclusion threshold, such as 1.0e-20, and a reasonably stringent exclusion threshold, say 1.0e-10. (The most stringent inclusion threshold possible in this query is 1.0e-300, and the least stringent exclusion threshold is 1.0e-3.) Proteobacterial subdivisions are classified by us as taxonomic level 3, so we select level 3. We don't care about matches outside the Proteobacteria, so we select "Ignore...". Performing this query on May 16, 2002, we get 183 ORFs (out of H. influenzae's 1709). Breaking this down into specific hits, we get 70 ORFs that are shared exclusively with alpha proteobacteria, 91 that are shared exclusively with beta proteobacteria, none with delta proteobacteria (no delta proteobacterial genome has yet been completed), and 22 that are shared exclusively with epsilon proteobacteria.

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