I want to map all the protein names form orthoMCL5 groups to Ensembl. I need it for basal metazoa such as Nematostella and Trichoplax. However the names in orthoMCL are from the JGI database and do not match the ENSEMBL names - how to do it? - I am sure that the ENSEMBL protein are derived from the JGI databases - so How did they translated the names? It will be better to get a code in Python which is my favorite language, but other solutions will be great.
This is correct since Ensembl Metazoa attempts to give all classes of objects a unique identifier. When you have IDs like
fgenesh1_pg.scaffold_688000001, an identifier assigned by FGENSH, the chances of clashing IDs is very high. You will see this pattern in all Ensembl Genomes databases where Ensembl Genomes has not taken responsibility for the generation of stable ids.