Articles liés à SHsearch. A Method for Fast Remote Homology Detection
Synopsis
Master's Thesis from the year 2014 in the subject Mathematics - Statistics, grade: 3.8, language: English, abstract: Remote homology detection is the problem of detecting homology in cases of low sequence similarity. It is a hard computational problem with no approach that works well in all cases. Methods based on profile hidden Markov models (HMM) often exhibit relatively higher sensitivity for detecting remote homologies than commonly used approaches. However, calculating similarity scores in profile HMM methods is computationally intensive as they use dynamic programming algorithms. In this paper, we introduce SHsearch: a new method for remote protein homology detection. Our method is implemented as a modification of HHsearch: a remote protein homology detection method based on comparing two profile HMMs. The motivation for modification was to reduce the run time of HHsearch significantly with minimal sensitivity loss. SHsearch focuses on comparing the important submodels of the query and database HMMs instead of comparing the complete models. Hence, SHsearch achieves a significant speedup over HHsearch with minimal loss in sensitivity. On S C O P 1.63, SHsearch achieved 88x speedup with 8.2% loss in sensitivity with respect to HHsearch at an error rate of 10%, which is deemed to be an acceptable tradeoff.
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SHsearch. A Method for Fast Remote Homology Detection
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Taschenbuch. Etat : Neu. Druck auf Anfrage Neuware - Printed after ordering - Master's Thesis from the year 2014 in the subject Mathematics - Statistics, grade: 3.8, , language: English, abstract: Remote homology detection is the problem of detecting homology in cases of low sequence similarity. It is a hard computational problem with no approach that works well in all cases. Methods based on profile hidden Markov models (HMM) often exhibit relatively higher sensitivity for detecting remote homologies than commonly used approaches. However, calculating similarity scores in profile HMM methods is computationally intensive as they use dynamic programming algorithms. In this paper, we introduce SHsearch: a new method for remote protein homology detection. Our method is implemented as a modification of HHsearch: a remote protein homology detection method based on comparing two profile HMMs. The motivation for modification was to reduce the run time of HHsearch significantly with minimal sensitivity loss. SHsearch focuses on comparing the important submodels of the query and database HMMs instead of comparing the complete models. Hence, SHsearch achieves a significant speedup over HHsearch with minimal loss in sensitivity. On S C O P 1.63, SHsearch achieved 88x speedup with 8.2% loss in sensitivity with respect to HHsearch at an error rate of 10%, which is deemed to be an acceptable tradeoff. N° de réf. du vendeur 9783668534490
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SHsearch. A Method for Fast Remote Homology Detection
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Taschenbuch. Etat : Neu. This item is printed on demand - it takes 3-4 days longer - Neuware -Master's Thesis from the year 2014 in the subject Mathematics - Statistics, grade: 3.8, , language: English, abstract: Remote homology detection is the problem of detecting homology in cases of low sequence similarity. It is a hard computational problem with no approach that works well in all cases. Methods based on profile hidden Markov models (HMM) often exhibit relatively higher sensitivity for detecting remote homologies than commonly used approaches. However, calculating similarity scores in profile HMM methods is computationally intensive as they use dynamic programming algorithms. In this paper, we introduce SHsearch: a new method for remote protein homology detection. Our method is implemented as a modification of HHsearch: a remote protein homology detection method based on comparing two profile HMMs. The motivation for modification was to reduce the run time of HHsearch significantly with minimal sensitivity loss. SHsearch focuses on comparing the important submodels of the query and database HMMs instead of comparing the complete models. Hence, SHsearch achieves a significant speedup over HHsearch with minimal loss in sensitivity. On S C O P 1.63, SHsearch achieved 88x speedup with 8.2% loss in sensitivity with respect to HHsearch at an error rate of 10%, which is deemed to be an acceptable tradeoff. 28 pp. Englisch. N° de réf. du vendeur 9783668534490
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SHsearch. A Method for Fast Remote Homology Detection
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ISBN 10 : 3668534497
ISBN 13 : 9783668534490
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Taschenbuch. Etat : Neu. Neuware -Master's Thesis from the year 2014 in the subject Mathematics - Statistics, grade: 3.8, , language: English, abstract: Remote homology detection is the problem of detecting homology in cases of low sequence similarity. It is a hard computational problem with no approach that works well in all cases. Methods based on profile hidden Markov models (HMM) often exhibit relatively higher sensitivity for detecting remote homologies than commonly used approaches. However, calculating similarity scores in profile HMM methods is computationally intensive as they use dynamic programming algorithms. In this paper, we introduce SHsearch: a new method for remote protein homology detection. Our method is implemented as a modification of HHsearch: a remote protein homology detection method based on comparing two profile HMMs. The motivation for modification was to reduce the run time of HHsearch significantly with minimal sensitivity loss. SHsearch focuses on comparing the important submodels of the query and database HMMs instead of comparing the complete models. Hence, SHsearch achieves a significant speedup over HHsearch with minimal loss in sensitivity. On S C O P 1.63, SHsearch achieved 88x speedup with 8.2% loss in sensitivity with respect to HHsearch at an error rate of 10%, which is deemed to be an acceptable tradeoff.BoD - Books on Demand, In de Tarpen 42, 22848 Norderstedt 28 pp. Englisch. N° de réf. du vendeur 9783668534490
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SHsearch. A Method for Fast Remote Homology Detection
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Taschenbuch. Etat : Neu. SHsearch. A Method for Fast Remote Homology Detection | Mohamed Baddar (u. a.) | Taschenbuch | 28 S. | Englisch | 2017 | GRIN Verlag | EAN 9783668534490 | Verantwortliche Person für die EU: BoD - Books on Demand, In de Tarpen 42, 22848 Norderstedt, info[at]bod[dot]de | Anbieter: preigu. N° de réf. du vendeur 110063203
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