FPGA acceleration of DNA sequence alignment: design analysis and optimization

Existing FPGA accelerators for short read mapping often fail to utilize the complete biological information in sequencing data for simple hardware design, leading to missed or incorrect alignment. In this work, we propose a runtime reconfigurable alignment pipeline that considers all information in sequencing data for the biologically accurate acceleration of short read mapping. We focus our efforts on accelerating two string matching techniques: FM-index and the Smith-Waterman algorithm with the affine-gap model which are commonly used in short read mapping. We further optimize the FPGA hardware using a design analyzer and merger to improve alignment performance. The contributions of this work are as follows. 1. We accelerate the exact-match and mismatch alignment by leveraging the FM-index technique. We optimize memory access by compressing the data structure and interleaving the access with multiple short reads. The FM-index hardware also considers complete information in the read data to maximize accuracy. 2. We propose a seed-and-extend model to accelerate alignment with indels. The FM-index hardware is extended to support the seeding stage while a Smith-Waterman implementation with the affine-gap model is developed on FPGA for the extension stage. This model can improve the efficiency of indel alignment with comparable accuracy versus state-of-the-art software. 3. We present an approach for merging multiple FPGA designs into a single hardware design, so that multiple place-and-route tasks can be replaced by a single task to speed up functional evaluation of designs. We first experiment with this approach to demonstrate its feasibility for different designs. Then we apply this approach to optimize one of the proposed FPGA aligners for better alignment performance.Open Acces

Design and Evaluation of a BLAST Ungapped Extension Accelerator, Master\u27s Thesis

The amount of biosequence data being produced each year is growing exponentially. Extracting useful information from this massive amount of data is becoming an increasingly difficult task. This thesis focuses on accelerating the most widely-used software tool for analyzing genomic data, BLAST. This thesis presents Mercury BLAST, a novel method for accelerating searches through massive DNA databases. Mercury BLAST takes a streaming approach to the BLAST computation by offloading the performance-critical sections onto reconfigurable hardware. This hardware is then used in combination with the processor of the host system to deliver BLAST results in a fraction of the time of the general-purpose processor alone. Mercury BLAST makes use of new algorithms combined with reconfigurable hardware to accelerate BLAST-like similarity search. An evaluation of this method for use in real BLAST-like searches is presented along with a characterization of the quality of results associated with using these new algorithms in specialized hardware. The primary focus of this thesis is the design of the ungapped extension stage of Mercury BLAST. The architecture of the ungapped extension stage is described along with the context of this stage within the Mercury BLAST system. The design is compact and performs over 20× faster than that of the standard software ungapped extension, yielding close to 50× speedup over the complete software BLAST application. The quality of Mercury BLAST results is essentially equivalent to the standard BLAST results

Design for novel enhanced weightless neural network and multi-classifier.

Weightless neural systems have often struggles in terms of speed, performances, and memory issues. There is also lack of sufficient interfacing of weightless neural systems to others systems. Addressing these issues motivates and forms the aims and objectives of this thesis. In addressing these issues, algorithms are formulated, classifiers, and multi-classifiers are designed, and hardware design of classifier are also reported. Specifically, the purpose of this thesis is to report on the algorithms and designs of weightless neural systems. A background material for the research is a weightless neural network known as Probabilistic Convergent Network (PCN). By introducing two new and different interfacing method, the word "Enhanced" is added to PCN thereby giving it the name Enhanced Probabilistic Convergent Network (EPCN). To solve the problem of speed and performances when large-class databases are employed in data analysis, multi-classifiers are designed whose composition vary depending on problem complexity. It also leads to the introduction of a novel gating function with application of EPCN as an intelligent combiner. For databases which are not very large, single classifiers suffices. Speed and ease of application in adverse condition were considered as improvement which has led to the design of EPCN in hardware. A novel hashing function is implemented and tested on hardware-based EPCN. Results obtained have indicated the utility of employing weightless neural systems. The results obtained also indicate significant new possible areas of application of weightless neural systems

"Going back to our roots": second generation biocomputing

Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative" solutions to human-defined problems. However, in this position paper we argue that the time has now come for a reassessment of how we exploit biology to generate new computational systems. Previous solutions (the "first generation" of biocomputing techniques), whilst reasonably effective, are crude analogues of actual biological systems. We believe that a new, inherently inter-disciplinary approach is needed for the development of the emerging "second generation" of bio-inspired methods. This new modus operandi will require much closer interaction between the engineering and life sciences communities, as well as a bidirectional flow of concepts, applications and expertise. We support our argument by examining, in this new light, three existing areas of biocomputing (genetic programming, artificial immune systems and evolvable hardware), as well as an emerging area (natural genetic engineering) which may provide useful pointers as to the way forward.Comment: Submitted to the International Journal of Unconventional Computin

Towards the Evolution of Novel Vertical-Axis Wind Turbines

Renewable and sustainable energy is one of the most important challenges currently facing mankind. Wind has made an increasing contribution to the world's energy supply mix, but still remains a long way from reaching its full potential. In this paper, we investigate the use of artificial evolution to design vertical-axis wind turbine prototypes that are physically instantiated and evaluated under approximated wind tunnel conditions. An artificial neural network is used as a surrogate model to assist learning and found to reduce the number of fabrications required to reach a higher aerodynamic efficiency, resulting in an important cost reduction. Unlike in other approaches, such as computational fluid dynamics simulations, no mathematical formulations are used and no model assumptions are made.Comment: 14 pages, 11 figure

Navigation for automatic guided vehicles using omnidirectional optical sensing

Thesis (M. Tech. (Engineering: Electrical)) -- Central University of technology, Free State, 2013Automatic Guided Vehicles (AGVs) are being used more frequently in a manufacturing environment. These AGVs are navigated in many different ways, utilising multiple types of sensors for detecting the environment like distance, obstacles, and a set route. Different algorithms or methods are then used to utilise this environmental information for navigation purposes applied onto the AGV for control purposes. Developing a platform that could be easily reconfigured in alternative route applications utilising vision was one of the aims of the research. In this research such sensors detecting the environment was replaced and/or minimised by the use of a single, omnidirectional Webcam picture stream utilising an own developed mirror and Perspex tube setup. The area of interest in each frame was extracted saving on computational recourses and time. By utilising image processing, the vehicle was navigated on a predetermined route. Different edge detection methods and segmentation methods were investigated on this vision signal for route and sign navigation. Prewitt edge detection was eventually implemented, Hough transfers used for border detection and Kalman filtering for minimising border detected noise for staying on the navigated route. Reconfigurability was added to the route layout by coloured signs incorporated in the navigation process. The result was the manipulation of a number of AGV’s, each on its own designated coloured signed route. This route could be reconfigured by the operator with no programming alteration or intervention. The YCbCr colour space signal was implemented in detecting specific control signs for alternative colour route navigation. The result was used generating commands to control the AGV through serial commands sent on a laptop’s Universal Serial Bus (USB) port with a PIC microcontroller interface board controlling the motors by means of pulse width modulation (PWM). A total MATLAB® software development platform was utilised by implementing written M-files, Simulink® models, masked function blocks and .mat files for sourcing the workspace variables and generating executable files. This continuous development system lends itself to speedy evaluation and implementation of image processing options on the AGV. All the work done in the thesis was validated by simulations using actual data and by physical experimentation