Manual Ortholog Curation
PomBase derives manually curated orthologs from a variety of sources. In some cases the consensus ortholog from the major ortholog predictors (Compara, Inparanoid, OrthoMCL) is used. Many distant orthologs have also been identified by PSI-BLAST matches that are uniformly one-to one across species (described in detail in reference [1]); these alignments have been submitted to the Pfam protein family database. Other ortholog predictions come from experimental data demonstrating functional correspondence or involving membership of corresponding complexes. These predictions are also aligned and submitted to Pfam before inclusion. PomBase's approach ensures that the breadth of coverage is greater than any individual prediction method, and includes many ortholog calls which are not detected by any automated method. Gradually, we will add and display supporting references for all orthology calls. [1] V. Wood (2006), Schizosaccharomyces pombe comparative genomics; from sequence to systems. In: Comparative Genomics Using Fungi as Models (P. Sunnerhagen and J. Piskur, eds.), Topics in Current Genetics 15:233-285.
PomBase curators