Review of Nineteenth-Century Geographies: The Transformation of Space from the Victorian Age to the American Century, eds. H. Michie and R. Thomas

It is by now a banal observation that published collections of conference papers tend to add up to a whole that is considerably less than the sum of the parts. Nineteenth-Century Geographies, a book that grew out of an interdisciplinary conference held at Rice University in 1998 falls into this category. While assuring my readers that each individual contribution is independently worth a read is likewise a predictable cliché, it is in fact the case that every one of the 17 articles collected here—notwithstanding the rather convoluted Introduction—has much to offer the study, broadly speaking, of ‘cultural spaces’ of British and American imperialisms in the nineteenth century. . . . All of my complaints aside, this turns out to be a much more enjoyable book to read than to review, and I would recommend skimming and dipping at length. I cannot quite imagine when a read-through of this book might be called for, except perhaps in graduate seminars on related topics.

Utilization of Probabilistic Models in Short Read Assembly from Second-Generation Sequencing

With the advent of cheaper and faster DNA sequencing technologies, assembly methods have greatly changed. Instead of outputting reads that are thousands of base pairs long, new sequencers parallelize the task by producing read lengths between 35 and 400 base pairs. Reconstructing an organism’s genome from these millions of reads is a computationally expensive task. Our algorithm solves this problem by organizing and indexing the reads using n-grams, which are short, fixed-length DNA sequences of length n. These n-grams are used to efficiently locate putative read joins, thereby eliminating the need to perform an exhaustive search over all possible read pairs. Our goal was develop a novel n-gram method for the assembly of genomes from next-generation sequencers. Specifically, a probabilistic, iterative approach was utilized to determine the most likely reads to join through development of a new metric that models the probability of any two arbitrary reads being joined together. Tests were run using simulated short read data based on randomly created genomes ranging in lengths from 10,000 to 100,000 nucleotides with 16 to 20x coverage. We were able to successfully re-assemble entire genomes up to 100,000 nucleotides in length.