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.

THE ASSOCIATION OF SEQUENCE OF HIRING PRACTICE AND BIOPHYSICAL COMPONENTS IN SCREENING PROBATIONARY FIREFIGHTERS

Variation in hiring procedures occurs within fire service human resource departments. In this study, City 1 and City 2 applicants were required to pass their biophysical assessments prior to being hired as firefighters at the beginning and end of the screening process, respectively. City 1 applicants demonstrated significantly lower resting heart rate (RHR), resting diastolic blood pressure (RDBP), body fat% (BF) and higher z-scores for BF, trunk flexibility (TF) and overall clinical assessment (p<0.05). Regression analysis found that age and conducting the biophysical assessment at the end of the screening process explained poorer biophysical assessment results in BF% (R2=21%), BF z-score (R2=22%), TF z-score (R2=10%) and overall clinical assessment z-score (R2=7%). Each of RHR (OR=1.06, CI=1.01-1.10), RDBP (OR=1.05, CI=1.00-1.11) and BF% (OR=1.20, CI=1.07-1.37) increased the odds of being a City 2 firefighter (p<0.05). Biophysical screening at the end of the hiring process may result in the hiring of a less healthy firefighter.

Complete Genome Sequence of Erwinia amylovora Bacteriophage

The complete genome of an Erwinia amylovora bacteriophage, vB_EamM_Ea35-70 (Ea35-70), is 271,084 bp, encodes 318 putative proteins, and contains one tRNA. Comparative analysis with other Myoviridae genomes suggests that Ea35-70 is related to the Phikzlikevirus genus within the family Myoviridae, since 26% of Ea35-70 proteins share homology to proteins in Pseudomonas phage φKZ.