BioBIKE
(COMMON-ORTHOLOGS-OF organism-list [PRIMARY organism])
(COMMON-ORTHOLOGS-OF (organism1 organism2 ...))
- Returns orthologs common to all organisms in the given list
- If a PRIMARY organism is specified, the common orthologs are given in terms of that organism; otherwise the first organism in the list is used
- Given-organisms may be given as a single variable holding a list or as multiple organisms between parentheses
- "Ortholog" is operationally defined through the ORTHOLOG-OF function with the threshold set to 1e-10
- Since the lists are precomputed (so that results are returned almost instantaneously), the threshold cannot be changed. If you want a different threshold, use ORTHOLOG-OF within a loop.
Example:
(COMMON-ORTHOLOGS-OF *loaded-organisms* PRIMARY S6803)
[Result is a list of proteins within Synechocystis PCC6803 with orthologs in all cyanobacteria
known to BioBIKE
Example:
(DEFINE het-core-genes AS
(COMMON-ORTHOLOGS-OF (Npun A7120 Avar) DISPLAY off)
[Result is a list of proteins within N. punctiforme with orthologs found in Anabaena PCC7120
and A. variabilis