We are trying to identify genes conserved in 5 specific eukaryotic species including C. elegans but not in 3 other certain eukaryotic species.
Is there a way to do it with some websites?
Or is there a program from somewhere tailored for this?
Your suggestions will be appreciated.
that depends on the other 3 eukaryotic species.
I know that Inparanoid, TreeFam, the Orthology Matrix (OMA) as well as EnsEMBL Compara have C.elegans data from the WS200 frozen release. Depending on which other species you are including, some or all of them might cover them in their sets. Querying is of course dependent on their respective web interface.
Personally I like the EnsMart interface from EnsEMBL best, but they cut down the functionality of the comparative side recently. Just try all of them and have a look at their supporting papers to have a rough idea who does what and why.
Technically speaking, we also import their data back into WormBase (that is what drives the Ortholog / Paralog section of the gene pages and the disease/other ortholog page). But so far we don’t have a web-interface to query it (ok, you can query the diseases).
Of course you could run some AQL queries agains the database to get the data, and for that we have search page, but it needs some understanding of the underlying data structures.
Thanks for the quick reply. I did try Inparanoid because it seems to cover all the genome we need. However, Inparanoid only does two genome comparison. I was trying to use Multiparanoid but they don’t have a web query interface.
I am not an expert on the Inparanoid web interface, but they make their species pairs available as XML files for download.
Maybe you can try to parse them?
And have a look at the other websites too.