Improving Short DNA Sequence Alignment with Parallel Computing

Variations in different types of genomes have been found to be responsible for a large degree of physical diversity such as appearance and susceptibility to disease. Identification of genomic variations is difficult and can be facilitated through computational analysis of DNA sequences. Newly available technologies are able to sequence billions of DNA base pairs relatively quickly. These sequences can be used to identify variations within their specific genome but must be mapped to a reference sequence first. In order to align these sequences to a reference sequence, we require mapping algorithms that make use of approximate string matching and string indexing methods. To date, few mapping algorithms have been tailored to handle the massive amounts of output generated by newly available sequencing technologies. In otrder to handle this large amount of data, we modified the popular mapping software BWA to run in parallel using OpenMPI. Parallel BWA matches the efficiency of multithreaded BWA functions while providing efficient parallelism for BWA functions that do not currently support multithreading. Parallel BWA shows significant wall time speedup in comparison to multithreaded BWA on high-performance computing clusters, and will thus facilitate the analysis of genome sequencing data.

Automatic Preparation of ETD Material from the Internet Archive for the DSpace Repository Platform

A big challenge associated with getting an institutional repository off the ground is getting content into it. This article will look at how to use digitization services at the Internet Archive alongside software utilities that the author developed to automate the harvesting of scanned dissertations and associated Dublin Core XML files to create an ETD Portal using the DSpace platform. The end result is a metadata-rich, full-text collection of theses that can be constructed for little out of pocket cost.