Academic Journal
An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty.
| Τίτλος: | An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty. |
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| Συγγραφείς: | Penn, Osnat, Privman, Eyal, Landan, Giddy, Graur, Dan, Pupko, Tal |
| Πηγή: | Molecular Biology & Evolution; Aug2010, Vol. 27 Issue 8, p1759-1767, 9p, 3 Diagrams, 4 Graphs |
| Περίληψη: | Multiple sequence alignment (MSA) is the basis for a wide range of comparative sequence analyses from molecular phylogenetics to 3D structure prediction. Sophisticated algorithms have been developed for sequence alignment, but in practice, many errors can be expected and extensive portions of the MSA are unreliable. Hence, it is imperative to understand and characterize the various sources of errors in MSAs and to quantify site-specific alignment confidence. In this paper, we show that uncertainties in the guide tree used by progressive alignment methods are a major source of alignment uncertainty. We use this insight to develop a novel method for quantifying the robustness of each alignment column to guide tree uncertainty. We build on the widely used bootstrap method for perturbing the phylogenetic tree. Specifically, we generate a collection of trees and use each as a guide tree in the alignment algorithm, thus producing a set of MSAs. We next test the consistency of every column of the MSA obtained from the unperturbed guide tree with respect to the set of MSAs. We name this measure the “GUIDe tree based AligNment ConfidencE” (GUIDANCE) score. Using the Benchmark Alignment data BASE benchmark as well as simulation studies, we show that GUIDANCE scores accurately identify errors in MSAs. Additionally, we compare our results with the previously published Heads-or-Tails score and show that the GUIDANCE score is a better predictor of unreliably aligned regions. [ABSTRACT FROM PUBLISHER] |
| Copyright of Molecular Biology & Evolution is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Βάση Δεδομένων: | Complementary Index |
| FullText | Links: – Type: other Text: Availability: 0 |
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| Header | DbId: edb DbLabel: Complementary Index An: 52553457 RelevancyScore: 834 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 833.7734375 |
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| Items | – Name: Title Label: Title Group: Ti Data: An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Penn%2C+Osnat%22">Penn, Osnat</searchLink><br /><searchLink fieldCode="AR" term="%22Privman%2C+Eyal%22">Privman, Eyal</searchLink><br /><searchLink fieldCode="AR" term="%22Landan%2C+Giddy%22">Landan, Giddy</searchLink><br /><searchLink fieldCode="AR" term="%22Graur%2C+Dan%22">Graur, Dan</searchLink><br /><searchLink fieldCode="AR" term="%22Pupko%2C+Tal%22">Pupko, Tal</searchLink> – Name: TitleSource Label: Source Group: Src Data: Molecular Biology & Evolution; Aug2010, Vol. 27 Issue 8, p1759-1767, 9p, 3 Diagrams, 4 Graphs – Name: Abstract Label: Abstract Group: Ab Data: Multiple sequence alignment (MSA) is the basis for a wide range of comparative sequence analyses from molecular phylogenetics to 3D structure prediction. Sophisticated algorithms have been developed for sequence alignment, but in practice, many errors can be expected and extensive portions of the MSA are unreliable. Hence, it is imperative to understand and characterize the various sources of errors in MSAs and to quantify site-specific alignment confidence. In this paper, we show that uncertainties in the guide tree used by progressive alignment methods are a major source of alignment uncertainty. We use this insight to develop a novel method for quantifying the robustness of each alignment column to guide tree uncertainty. We build on the widely used bootstrap method for perturbing the phylogenetic tree. Specifically, we generate a collection of trees and use each as a guide tree in the alignment algorithm, thus producing a set of MSAs. We next test the consistency of every column of the MSA obtained from the unperturbed guide tree with respect to the set of MSAs. We name this measure the “GUIDe tree based AligNment ConfidencE” (GUIDANCE) score. Using the Benchmark Alignment data BASE benchmark as well as simulation studies, we show that GUIDANCE scores accurately identify errors in MSAs. Additionally, we compare our results with the previously published Heads-or-Tails score and show that the GUIDANCE score is a better predictor of unreliably aligned regions. [ABSTRACT FROM PUBLISHER] – Name: Abstract Label: Group: Ab Data: <i>Copyright of Molecular Biology & Evolution is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1093/molbev/msq066 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 9 StartPage: 1759 Titles: – TitleFull: An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Penn, Osnat – PersonEntity: Name: NameFull: Privman, Eyal – PersonEntity: Name: NameFull: Landan, Giddy – PersonEntity: Name: NameFull: Graur, Dan – PersonEntity: Name: NameFull: Pupko, Tal IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 08 Text: Aug2010 Type: published Y: 2010 Identifiers: – Type: issn-print Value: 07374038 Numbering: – Type: volume Value: 27 – Type: issue Value: 8 Titles: – TitleFull: Molecular Biology & Evolution Type: main |
| ResultId | 1 |