Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 16 of 16 for “"Smith-Waterman"”.
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MR-CUDASW - GPU accelerated Smith-Waterman algorithm for medium-length (meta)genomic data
… by using a GPU-based implementation of the Smith-Waterman algorithm. In this thesis an existing GPU-accelerated sequence alignment algorithm is adapted and expanded to reduce its completion time. A number of improvements and changes are made to the original software. Workload distribution, …
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Exploiting Multigrain Parallelism in Pairwise Sequence Search on Emergent CMP Architectures
… a dynamic programming algorithm called Smith-Waterman both within and across multiple Cell Broadband Engines and within an nVIDIA GeForce General Purpose Graphics Processing Unit (GPGPU). Cell Broadband Engine: We parallelize the Smith-Waterman algorithm within a Cell node by performing …
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Exact genome alignment
… method and SSEARCH, a slower but more rigorous Smith-Waterman based approach, on whole genome sequences from primates and mammals. An exact genome alignment technique is used by breaking the entire genome into fragments and aligning these fragments with the reference genome using the …
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Enabling the use of Heterogeneous Computing for Bioinformatics
… a highly efficient dynamic programming based Smith-Waterman kernel is implemented in hardware, which is able to achieve a peak throughput of 307.2 Giga Cell Updates per Second (GCUPS) on Convey HC-1. A dynamic programming accelerator interface is provided to any application that uses …
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Matching Genetic Sequences in Distributed Adaptive Computing Systems
… reconfigurable FPGA implementation of the Smith-Waterman similarity comparison algorithm. Additionally, this thesis presents tools designed for the ACS API that assist developers creating applications in a heterogeneous distributed adaptive computing environment.
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Comparative analysis of algorithms for identifying copy number variation in array CGH data
… segmentation (CBS), CGH segmentation, Price —Smith—Waterman algorithm (the three algorithms are a part of ADaCGH tool) and Cluster Along Chromosome (CLAC) which is not publicly available were studied and used for the analysis of array CGH data. Simulated data set was generated by adding …
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Searching Biological Sequence Databases Using Distributed Adaptive Computing
… technologies. The search is performed using the Smith-Waterman algorithm, a common sequence comparison algorithm. To reduce the total search time, an initial search is performed using a version of the algorithm, implemented in adaptive computing hardware, which is designed to efficiently perform …
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FPGA-Based Accelerator Development for Non-Engineers
… made significant modifications to a bare-bones Smith-Waterman accelerator, extending functionality and improving performance.
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Algorithms for pre-microrna classification and a GPU program for whole genome comparison
… are called anchors. A rigorous method named Smith-Waterman search is applied for the anchor seeking, but takes days and months to map millions of bases for mammalian genome sequences. With GPU programming, which is designed to run in parallel hundreds of short functions called threads, up to …
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Approximate string matching methods for duplicate detection and clustering tasks
… using several re- scorers: HD with Normalized Smith-Waterman Re-scorer, HD with TFIDF and Jaccard re-scorers, HD with the Longest Common Prefix and TFIDF re-scorers, and HD with the Unweighted Longest Common Prefix Re-scorer. Another contribution of this dissertation includes the extensive …
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Algorithms in comparative genomics
… on real data than the widely used BLAST and Smith- Waterman algorithms. Within the realm of comparative genomics are also a large number of recently conducted GWAS. GWAS aim to identify regions in the genome that are associated with a given disease. The support vector machine (SVM) provides a …
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The encapsidation protein from Lactococcus lactis asccφ28 as a novel system for the study of molecular motors
… to homogeneity (55.6% sequence similarity, Smith-Waterman score). Size-exclusion chromatography suggests that the recombinant protein forms a single oligomeric species in solution, while analytical ultracentrifugation and small-angle x-ray studies reveal a decameric stoichiometry. …
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Analysis of the impact of sequencing errors on BLAST using fault injection
… while SSEARCH is based on the optimal Smith-Waterman algorithm. The error rates were larger than the corresponding fault rates by one to two orders of magnitude, indicating a small error rate in the sequence can drastically change the analysis output. False negative (FN) error rates …
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Efficient parallelization of Bowtie 2 with OpenCL on GPU
As a crucial and computation-intensive aspect in bioinformatics, sequence alignment has gained considerable attention from researchers and developers. Among all the sequence aligners, Bowtie 2 is one of the most commonly used, due to its high speed and accuracy. This thesis presents a parallel …
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Generalizing the Utility of Graphics Processing Units in Large-Scale Heterogeneous Computing Systems
Today, heterogeneous computing systems are widely used to meet the increasing demand for high-performance computing. These systems commonly use powerful and energy-efficient accelerators to augment general-purpose processors (i.e., CPUs). The graphic processing unit (GPU) is one such accelerator. …
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Communication avoiding parallel algorithms for amorphous problems
Parallelizing large sized problem in parallel systems has always been a challenge for programmer. This difficulty is caused by the complexity of the existing systems as well as the target problems. This is becoming a greater issue as the data sizes are constantly growing and as a result, larger …