Biomedical subjects

Michael Cameron

Publications and source records attributed to Michael Cameron.

3 recordsLinked to original sources

PubMed2006

A deterministic finite automaton for faster protein hit detection in BLAST.

BLAST is the most popular bioinformatics tool and is used to run millions of queries each day. However, evaluating such queries is slow, taking typically minutes on modern workstations. Therefore, continuing evolution of BLAST--by improving its algorithms and optimizations--is essential to improve search times in the face of exponentially increasing collection sizes. We present an optimization to the first stage of the BLAST algorithm specifically designed for protein search. It produces the same results as NCBI-BLAST but in around 59% of the time on Intel-based platforms; we also present results for other popular architectures. Overall, this is a saving of around 15% of the total typical BLAST search time. Our approach uses a deterministic finite automaton (DFA), inspired by the original scheme used in the 1990 BLAST algorithm. The techniques are optimized for modern hardware, making careful use of cache-conscious approaches to improve speed. Our optimized DFA approach has been integrated into a new version of BLAST that is freely available for download at http://www.fsa-blast.org/.

Algorithms↗

PubMed2006

Sleep and aggression in substance-abusing adolescents: results from an integrative behavioral sleep-treatment pilot program.

STUDY OBJECTIVE: To examine whether change in total sleep time during an integrative, behavioral sleep intervention is associated with aggression. Specifically, we tested whether adolescents who reported experiencing aggressive thoughts or actions after treatment had worse treatment trajectories (e.g., less total sleep time across treatment) than adolescents with no aggressive thoughts or actions after treatment. DESIGN: Nonpharmacologic open trial with 9 weeks of weekly assessment. SETTING: University of Arizona Sleep Research Laboratory PATIENTS OR PARTICIPANTS: Twenty-three adolescents recently treated for substance abuse in outpatient community centers. INTERVENTIONS: Six-week integrative, behavioral sleep intervention. MEASUREMENTS AND RESULTS: Weekly sleep-summary indexes were calculated from daily sleep diaries and entered as dependent variables in a series of growth-curve analyses. Statistically significant Session x Post-treatment Aggressive Ideation interactions emerged when predicting changes in total sleep time, gamma13 = 9.76 (SE = 4.12), p < .05, and time spent in bed, gamma13 = 10.08, (SE = 4.33), p < .05, even after controlling for aggressive ideation and the frequency of substance use, as assessed at baseline. A similar pattern of results was seen for self-reported aggressive actions occurring during conflicts. CONCLUSIONS: These pilot data suggest that inadequate sleep in substance-abusing adolescents may contribute to the experiencing of aggressive thoughts and actions. Limitations include a small sample size and a restricted assessment of aggression. Nonetheless, these findings lend preliminary support to the breadth of therapeutic effectiveness of an integrative, behavioral sleep-therapy program for adolescents with a history of substance abuse and related behaviors.

Adolescent↗

PubMedDate not supplied

Improved gapped alignment in BLAST.

Homology search is a key tool for understanding the role, structure, and biochemical function of genomic sequences. The most popular technique for rapid homology search is BLAST, which has been in widespread use within universities, research centers, and commercial enterprises since the early 1990s. In this paper, we propose a new step in the BLAST algorithm to reduce the computational cost of searching with negligible effect on accuracy. This new step-semigapped alignment-compromises between the efficiency of ungapped alignment and the accuracy of gapped alignment, allowing BLAST to accurately filter sequences with lower computational cost. In addition, we propose a heuristic-restricted insertion alignment-that avoids unlikely evolutionary paths with the aim of reducing gapped alignment cost with negligible effect on accuracy. Together, after including an optimization of the local alignment recursion, our two techniques more than double the speed of the gapped alignment stages in BLAST. We conclude that our techniques are an important improvement to the BLAST algorithm. Source code for the alignment algorithms is available for download at http://www.bsg.rmit.edu.au/iga/.

Algorithms↗