how to compare the genome of C.elegans and M. incognita

hello, here I want to compare the genome of C.elegans and M. incognita, as their genomes are published. Could anyone give me some suggestion? Thanks.

that depends on what you actually want to do:

  • do you want to look for conservation in the genomic sequence? Make and alignment of it with WABA / LAGAN / BLASTZ/…
  • do you want to compare the protein sets? Grab the one from INRA and cluster it with the C.elegans one (like as example with OrthoMCL).

As INRA hasn’t made the gene predictions public, but only their protein sequences, have a stroll trough to see what they got and have a look at our C.elegans data.

Also plan on what the goal of your experiment is supposed to be.