PHYLOGENETIC INFERENCE, GENE DISCOVERY AND FUNCTIONAL ANALYSIS WITHIN A REGION OF THE MAJOR HISTOCOMPATIBILITY COMPLEX

1. You are requested to investigate the evolutionary history of CFB and C2 through phylogenetic analysis of available protein sequences. These genes are paralogues, and hence share a common ancestral gene. You will download CFB, C2 and CFB/C2-like sequences from a number of species, multiply align them and infer phylogenetic trees using several methods. You will choose the ‘best’ representative tree and from this determine the likely timepoint of the CFB duplication event that led to the evolution of modern day mammalian C2. 2. You are requested to annotate a portion of the alpaca genome found in a scaffold with accession number KB632644 (available in GenBank also asRefSeq accession NW_005882912) in the region from bp 2507900 to bp 2603350, which will contain a number of genes from the MHC Class III region. You will use freely available software to predict the location of protein coding genes in the region, as well as report on the number of intespersed repetitive regions. You will compare your new gene annotation with the annotation currently available for this region, and note any differences. You will also report on the location of functional domains in the predicted protein products of the genes discovered. PLEASE READ THE ATTACHED FILE CAREFULLY BEFORE BIDDING