SHsearch. A Method for Fast Remote Homology Detection

Language: English

Published by GRIN Verlag, GRIN Verlag Okt 2017, 2017

3668534497 / 9783668534490

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This item is printed on demand - Print on Demand Titel. 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.Books on Demand GmbH, Überseering 33, 22297 Hamburg 28 pp. Englisch.

Seller Inventory # 9783668534490

Title
SHsearch. A Method for Fast Remote Homology Detection
Author
Mohamed Baddar
Publisher
GRIN Verlag, GRIN Verlag Okt 2017
Publication year
2017
Condition
Neu
Binding
Taschenbuch
Language
English
ISBN 10
3668534497
ISBN 13
9783668534490
Item weight
113 grams
Dimensions
297x210x3 mm

buchversandmimpf2000

Emtmannsberg, BAYE, Germany

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