A Study of Ordered Gene Problems Featuring DNA Error Correction and DNA Fragment Assembly with a Variety of Heuristics, Genetic Algorithm Variations, and Dynamic Representations

Ordered gene problems are a very common classification of optimization problems. Because of their popularity countless algorithms have been developed in an attempt to find high quality solutions to the problems. It is also common to see many different types of problems reduced to ordered gene style problems as there are many popular heuristics and metaheuristics for them due to their popularity. Multiple ordered gene problems are studied, namely, the travelling salesman problem, bin packing problem, and graph colouring problem. In addition, two bioinformatics problems not traditionally seen as ordered gene problems are studied: DNA error correction and DNA fragment assembly. These problems are studied with multiple variations and combinations of heuristics and metaheuristics with two distinct types or representations. The majority of the algorithms are built around the Recentering- Restarting Genetic Algorithm. The algorithm variations were successful on all problems studied, and particularly for the two bioinformatics problems. For DNA Error Correction multiple cases were found with 100% of the codes being corrected. The algorithm variations were also able to beat all other state-of-the-art DNA Fragment Assemblers on 13 out of 16 benchmark problem instances.

Improving grade eight students' spelling performance with a triad strategy approach

Thesis (M.Ed.)-- Brock University, 1996.

New Contig Creation Algorithm for the de novo DNA Assembly Problem

DNA assembly is among the most fundamental and difficult problems in bioinformatics. Near optimal assembly solutions are available for bacterial and small genomes, however assembling large and complex genomes especially the human genome using Next-Generation-Sequencing (NGS) technologies is shown to be very difficult because of the highly repetitive and complex nature of the human genome, short read lengths, uneven data coverage and tools that are not specifically built for human genomes. Moreover, many algorithms are not even scalable to human genome datasets containing hundreds of millions of short reads. The DNA assembly problem is usually divided into several subproblems including DNA data error detection and correction, contig creation, scaffolding and contigs orientation; each can be seen as a distinct research area. This thesis specifically focuses on creating contigs from the short reads and combining them with outputs from other tools in order to obtain better results. Three different assemblers including SOAPdenovo [Li09], Velvet [ZB08] and Meraculous [CHS+11] are selected for comparative purposes in this thesis. Obtained results show that this thesis’ work produces comparable results to other assemblers and combining our contigs to outputs from other tools, produces the best results outperforming all other investigated assemblers.

The effects of manipulated augmented sensory feedback on error detection when using a touch screen

The purpose of the present study was to determine which augmented sensory modality would best develop subjective error-detection capabilities of learners performing a spatial-temporal task when using a touch screen monitor. Participants were required to learn a 5-digit key-pressing task in a goal time of 2550 ms over 100 acquisition trials on a touch screen. Participants were randomized into 1 of 4 groups: 1) visual-feedback (colour change of button when selected), 2) auditory-feedback (click sound when button was selected), 3) visual-auditory feedback (both colour change and click sound when button was selected), and 4) no-feedback (no colour change or click sound when button was selected). Following each trial, participants were required to provide a subjective estimate regarding their performance time in relation to the actual time it took for them complete the 5-digit sequence. A no-KR retention test was conducted approximately 24-hours after the last completed acquisition trial. Results showed that practicing a timing task on a touch screen augmented with both visual and auditory information may have differentially impacted motor skill acquisition such that removal of one or both sources of augmented feedback did not result in a severe detriment to timing performance or error detection capabilities of the learner. The present study reflects the importance of multimodal augmented feedback conditions to maximize cognitive abilities for developing a stronger motor memory for subjective error-detection and correction capabilities.