GPU Acceleration of BWA-MEM DNA Sequence Alignment

Over the past 20 years, the cost of sequencing genomes has reduced drastically. As DNA data grows at an unprecedented rate, the need for fast and affordable software and hardware solutions for DNA analysis is higher than ever. A critical and time-consuming component in any DNA analysis pipeline is sequence alignment, which refers to mapping...

Log Differencing using State Machines for Anomaly Detection

Huge amounts of log data are generated every day by software. These data contain valuable information about the behavior and the health of the system, which is rarely exploited, because of their volume and unstructured nature. Manually going through log files is a time-consuming and labor-intensive procedure for developers. Nonetheless logging...

Viewpoint dependent model for multi-view object recognition

The life expectancy of humans increases due to better medical care, food quality and personal hygiene. The demand for domestic robots performing (simple) household chores will increase as consequence to this trend. An important task of these robots is recognizing objects within an environment. Object models are constructed using multiple views...

Computational Assessment of Single-Molecule Protein Sequencing

A single-molecule protein sequencer, which labels only 2 out of 20 amino acids and uses single-molecule TIRF microscopy to measure the order of these fingerprints, opens the door to identify proteins with high fidelity using only a small quantity of sample. From the fingerprint, a key challenge is to detect which protein was measured. We present...

Biological Sequence Alignment Using Graphics Processing Units

Alignment algorithms are used to find similarity between biological sequences, such as DNA and proteins. By aligning a sequence with a database, similar sequences can be found. These can be used to identify the source of a query sequence, to find commonalities between organisms, or to infer an ancestral relation. Various methods of performing...