Ensembl Compara - CNB - Protein Design Group

Load Genes and LongestTranslation from all species inEnsembl. 26 species in v41hoursWU Blastp + SmithWaterman longesttranslation of every Gene against everyother in a genome­wise mannerhours/daysBuild a graph of gene relationsbased on BRH 1 and BSR 2Extract the connected components(= single linkage clusters)2­3 days ­ 1CPUFor each cluster, build a multiplealignment (MUSCLE) based on theprotein sequenceshoursmultifurcated species treeReconcile each gene tree with thespecies tree to call duplicationevent on internal nodes (RAP)hoursv41From each alignment, build a genetree (PHYML)hours/daysInference of orthologs and paralogs(OrthoTree)hoursJul 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.