This is a project started for Erica Smith in CMB. We are comparing gene models at the protein level between S. med (planaria), worm, fly and human. The basic hypothesis is that there is functional conservation between S. med and H. sapiens that is not present between C. elegans and D. melanogaster and H. sapiens
We did a full set of BLAST rounds using RefSeq release 40 and Smed release 4 protein models, but it is very difficult to walk from the NCBI gene_ids to the corresponding homologene ids. We then tried comparing the Smed protein models with existing orthologue clusters using Ortho MCL.