Ensembl Compara - CNB - Protein Design Group

Load Genes and LongestTranslation from all species inEnsembl. 31? species in v42WU Blastp + SmithWaterman longesttranslation of every Gene against everyother in a genome­wise mannerBuild a graph of gene relationsbased on BRH 1 and BSR 2Extract the connected components(= single linkage clusters)For each cluster, build a multiplealignment (MUSCLE) based on theprotein sequencesInference of orthologs and paralogs(OrthoTree)From each alignment, build a geneand reconcile with the species treeto call duplication events oninternal nodes (NJTREE_PHYML)v42Jul 2007BSR: Blast Score Ratio. When 2 proteins P1 and P2 are compared,BSR=scoreP1P2/max(self­scoreP1 or self­scoreP2). The default threshold usedin the initial clustering step is 0.33.