Normalized global alignment for protein sequences
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Show full item recordcomunitat-uji-handle:10234/9
comunitat-uji-handle2:10234/43662
comunitat-uji-handle3:10234/43643
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http://dx.doi.org/10.1016/j.jtbi.2011.09.017 |
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Title
Normalized global alignment for protein sequencesDate
2011Publisher
ElsevierISSN
0022-5193Bibliographic citation
Journal of Theoretical Biology (Dec. 2011) vol. 291, p. 22-28Type
info:eu-repo/semantics/articlePublisher version
http://www.sciencedirect.com/science/article/pii/S0022519311004735Version
info:eu-repo/semantics/publishedVersionSubject
Abstract
Global alignment is used to compare proteins in different fields, for example in phylogenetic research. In order to reduce the length and composition dependence of global alignment scores, Z-score is computed with a ... [+]
Global alignment is used to compare proteins in different fields, for example in phylogenetic research. In order to reduce the length and composition dependence of global alignment scores, Z-score is computed with a Monte-Carlo algorithm. This technique requires a great number of sequence alignments on shuffled sequences, leading to a high computational cost. In this work, a normalized global alignment score is introduced in order to correct the length dependence of global alignments. This score is defined as the best ratio between the score of an alignment and its length, and an algorithm to compute it based on fractional programming is implemented. The properties and effectiveness of normalized global alignment applied toprotein comparison are analyzed.
Experiments with proteins selected from the SCOP ASTRAL database were run to study relationship of normalized global alignment with Z-score and performance in homologous detection. Results show that normalized global alignment has a computational cost equivalent to 2.5 Needleman-Wunsch runs and a linear relationship with Z-score. This linearity allows us to use normalized global alignment as a cheap substitute to a computationally expensive Z-score. Experiments show that normalized global alignment improves the ability to identify homologous proteins. [-]
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© 2011 Elsevier Inc. All rights reserved
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