Genomes …

Genomes are grouped by domain in the pop-up menus. First the Bacteria are listed, then the Archaea and then Eukaryota.

Within each domain genomes are listed in alphabetical order.

Genome query for

Lineage-specific, Group-specific and Species-specific ORFs

For any of the sequenced genomes, we identify all of its protein-coding genes which are specific to the genome's own lineage, at the specified depth and with the specified stringency.
Species-specific ORFs are sequences which cannot be found in any other species at the specified stringency, but may be found in other genomes of the same species.
Group-specific ORFs are sequences which can be found in one arbitrarily defined group, but not another.

Define the inclusion group as set#1, and the exclusion group as set#2, by adding or removing genomes from one of the following preselects:
A blank list.
All genomes preselected.
All archaeal genomes preselected.
All bacterial genomes preselected.

more information...

Choose a BLASTP cutoff e-value (1.0e-300 to 1.0e-3): 1.0e-

(You may select a range of BLASTP cutoff e-values for this analysis by entering first.last.step (e.g., 10.100.5 would result in 19 separate analyses, at 10, 15, 20, 25, ..., 95, 100. If you omit the final number (e.g. 10.100) the step size defaults to 10. If you enter only a single number (e.g. 10) the query runs a single analysis. Note that "Results from my last query" is not updated if you select a range of BLASTP e-values.))

Choose a reference genome, from which the database search is launched:

View its:

Lineage-specific ORFs, top-level taxonomic classification
Lineage-specific ORFs, second-level taxonomic classification
Lineage-specific ORFs, third-level taxonomic classification
Lineage-specific ORFs, fourth-level taxonomic classification
Species-specific ORFs
Non-species-specific ORFs
Group-specific ORFs, from the genome selected above
Group-specific ORFs, from each of the inclusion-set genomes in turn

If you selected group-specific ORFs above, enter the minimum number of genomes from your defined set#1 that must match an ORF above the inclusion threshold entered at the top of this form, and enter the exclusion threshold 1.0e- above which no more than genomes from your defined set#2 can match.

Use reciprocal-best-match in finding group-specific ORFs, instead of simple match.
Show which genomes were matched in the inclusion and exclusion sets respectively, as strings of 0 (absent) and 1 (present).

Notes:

Group-specific ORFs are currently found by simple match or reciprocal best match, whereas lineage-specific and species-specific ORFs are currently found by simple match only. Contact us if you would like the option to find lineage- or species-specific ORFs by reciprocal best match.
Lineage-specific ORFs must be found in at least one other species within that lineage in order to be considered: i.e., lineage-specific ORFs exclude species-specific ORFs.
Species-specific ORFs may not all represent real genes. Some may be "statistical ORFs".
Here is the list of our taxonomic classifications for each of the sequenced genomes.