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In the last decades there is an exponential growth in the amount of genomic data that need to be analyzed. A very important problem in biology is the extraction of the biologically functional genomic DNA from the actual genome of the organisms. There have been proposed many computational biology algorithms that solve the gene finding problem which utilize various approaches; GlimmerHMM is considered...
The graphics processing unit (GPU) has evolved from being a fixed-function processor with programmable stages into a programmable processor with many fixed-function components that deliver massive parallelism. By modifying the GPU's stream processor to support “general-purpose computation” on the GPU (GPGPU), applications that perform massive vector operations can realize many orders-of-magnitude...
In bioinformatics, alignments are commonly performed in genome and protein sequence analysis for gene identification and evolutionary similarities. There are several approaches for such analysis, each varying in accuracy and computational complexity. Smith-Waterman (SW) is by far the best algorithm for its accuracy in similarity scoring. However, execution time of this algorithm on general purpose...
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