Long time lurker, first time poster. I don't know what key words to even search for here:
I am trying to find all genes in a bacterial species X that seem to share similar motifs/evolutionary history, (were of the TetR or MarR family, etc). All of the software. I have sequences that are characteristic of these genes/protein sequence but any labeling of these gene products in a database is fairly limited. I was told to look into using orthology application to find paralogs in the species (genes created from a doubling event, not from a species splitting event). All of the applications I can find examine from inter (between) species view point but not from intraspecies (with-in a species) own genome. How might I go about doing this? what should I be looking for? Can I do this in Paranoid?