By B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan
This booklet provides an assessment method to layout destiny FPGA materials incorporating difficult embedded blocks (HEBs) to speed up purposes. this technique can be worthy for choice of blocks to be embedded into the cloth and for comparing the functionality achieve that may be accomplished through such an embedding. The authors illustrate using their method through learning the impression of HEBs on vital bioinformatics functions: protein docking and genome meeting. The booklet additionally explains how the respective HEBs are designed and the way implementation of the appliance is completed utilizing those HEBs. It indicates that major speedups might be completed over natural software program implementations through the use of such FPGA-based accelerators. The method offered during this e-book can also be used for designing HEBs for accelerating software program implementations in different domain names along with bioinformatics. This e-book will end up worthwhile to scholars, researchers, and practising engineers alike.
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Extra info for Architecture Exploration of FPGA Based Accelerators for BioInformatics Applications
The command gprof is run to get the details of the profiled data. It also generates a call graph showing the dynamic hierarchy of the program parts. The profile data lists the various functions that are executed along with the time taken and the number of times the function was executed. VTune and PIN are proprietary tools from Intel. VTune uses PIN tool in the background for getting the profile data. The tool has a good GUI and displays the call graph. The profile data is also displayed along with call graph.
Databases have been created and statistical analysis programs have been developed for retrieving specific information from this data. Sequence assembly is a computational biology problem where the reads generated from the NGS machine are used to build the whole genome. An example of assembly is shown in Fig. 7. A biological sample is preprocessed and given to a sequencing machine, which generates a set of short reads. These short reads are assembled to construct the genome. The ‘T’ in the read CTGTGTGTT, is an error as the exact match to the genome at that position was supposed to be ‘C’.
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Architecture Exploration of FPGA Based Accelerators for BioInformatics Applications by B. Sharat Chandra Varma, Kolin Paul, M. Balakrishnan