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.

The Resilience of Self-Esteem in Late Adulthood

OBJECTIVE: The authors examined the resilience of self-esteem after loss in the lives of older adults. Specifically, the authors investigated the relationship between loss and change in self-esteem during a 3-year period. METHOD: A subsample of older adults (n = 1,278) from the Americans' Changing Lives Study was used to examine loss in the domains of health, financial security, or work and career and self-esteem before and after the loss. RESULTS: There was a small but significant decrease in self-esteem between Wave I and Wave II of the study. Loss in one of the domains explained less than 1% of the variance in self-esteem change. DISCUSSION: The low incidence of loss and small change in high levels of self-esteem are further evidence of resilience in older adults' psychological well-being. The implications for older adults' use of cognitive strategies to manage losses and promote gains are discussed.