Please use this identifier to cite or link to this item:
https://ah.lib.nccu.edu.tw/handle/140.119/97015
DC Field | Value | Language |
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dc.contributor | 資科系 | - |
dc.creator | 張家銘 | zh_TW |
dc.creator | Chang, Jia-Ming | - |
dc.creator | Hsu*, Wen-Lian | en_US |
dc.creator | Sung*, Ting-Yi | en_US |
dc.creator | Notredame, Cédric | en_US |
dc.creator | Lin, Hsin-Nan | en_US |
dc.date | 2011-12 | - |
dc.date.accessioned | 2016-05-30T09:24:57Z | - |
dc.date.available | 2016-05-30T09:24:57Z | - |
dc.date.issued | 2016-05-30T09:24:57Z | - |
dc.identifier.uri | http://nccur.lib.nccu.edu.tw/handle/140.119/97015 | - |
dc.description.abstract | Most sequence alignment tools can successfully align protein sequences with higher levels of sequence identity. The accuracy of corresponding structure alignment, however, decreases rapidly when considering distantly related sequences (<20% identity). In this range of identity, alignments optimized so as to maximize sequence similarity are often inaccurate from a structural point of view. Over the last two decades, most multiple protein aligners have been optimized for their capacity to reproduce structure-based alignments while using sequence information. Methods currently available differ essentially in the similarity measurement between aligned residues using substitution matrices, Fourier transform, sophisticated profile-profile functions, or consistency-based approaches, more recently. In this paper, we present a flexible similarity measure for residue pairs to improve the quality of protein sequence alignment. Our approach, called SymAlign, relies on the identification of conserved words found across a sizeable fraction of the considered dataset, and supported by evolutionary analysis. These words are then used to define a position specific substitution matrix that better reflects the biological significance of local similarity. The experiment results show that the SymAlign scoring scheme can be incorporated within T-Coffee to improve sequence alignment accuracy. We also demonstrate that SymAlign is less sensitive to the presence of structurally non-similar proteins. In the analysis of the relationship between sequence identity and structure similarity, SymAlign can better differentiate structurally similar proteins from non- similar proteins. We show that protein sequence alignments can be significantly improved using a similarity estimation based on weighted n-grams. In our analysis of the alignments thus produced, sequence conservation becomes a better indicator of structural similarity. SymAlign also provides alignment visualization that can display sub-optimal alignments on dot-matrices. The visualization makes it easy to identify well-supported alternative alignments that may not have been identified by dynamic programming. SymAlign is available at http://bio-cluster.iis.sinica.edu.tw/SymAlign/. | - |
dc.format.extent | 396529 bytes | - |
dc.format.mimetype | application/pdf | - |
dc.relation | PLoS One, Vol.6, No.12, pp.e27872 | - |
dc.title | Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words | - |
dc.type | article | - |
dc.identifier.doi | 10.1371/journal.pone.0027872 | - |
dc.doi.uri | http://dx.doi.org/10.1371/journal.pone.0027872 | - |
item.openairecristype | http://purl.org/coar/resource_type/c_18cf | - |
item.openairetype | article | - |
item.fulltext | With Fulltext | - |
item.grantfulltext | restricted | - |
item.cerifentitytype | Publications | - |
Appears in Collections: | 期刊論文 |
Files in This Item:
File | Description | Size | Format | |
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Improving.pdf | 387.24 kB | Adobe PDF2 | View/Open |
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