Finishing Drosophila virilis Fosmid Clone 4N16

The overarching goal of Bio 4342/W research over the past several years has been to understand a euchromatic region of the Drosophila virilis genome well enough to be able to distinguish this domain at the DNA level from the heterochromatic counterparts in its genetic relatives, such as Drosophila melanogaster, the common fruit fly. The class will utilize the well-established genome of D. melanogaster as a model organism possessing a heterochromatic fourth chromosome for comparison. Current class research focuses on completing a reliable genome sequence for the equivalent “dot” chromosome in D. virilis in hopes of discerning sequence domains or gene characteristics that explain this inter-species difference in chromosomal organization. In this report, I describe sequence finishing for fosmid 4N16. Finishing Workflow To start off After running Phred/Phrap to call bases on the raw sequence data and create an initial assembly for my fosmid, I was presented with a Consed assembly consisting of five major contigs with a significant number of inconsistent forward/reverse pairs, a significant low coverage region and extensive misassembly. Running Crossmatch identifies direct sequence repeats, indicated by orange lines, or tandem sequence repeats, indicated by black lines (none visible here), according to a desired percent similarity. Viewing the Crossmatch results with a sequence similarity of 90% revealed very high sequence repetition throughout my entire fosmid. Figure 1.1 Initial assembly