finding genes of the same family in an organism/ intraspecies homolog discovery

Question

[bryantchambers]

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?

Thanks!

Answer 1

[lieven.sterck]

You mean InParanoid, right?

Yes you can, "trick" is to do the initial blast search as all vs all self blast(p) . You can actually do this with most (all?) protein clustering/orthology program. There is however still an advantage of using an (or more) additional species, this will increase the 'resolution' of the clustering and will result in more fine-grained families.