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Title: Some remarks on evaluating the quality of the multiple sequence alignment based on the BAliBASE benchmark
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Abstract:
BAliBASE is one of the most widely used benchmarks for multiple sequence alignment programs. The accuracy of alignment methods is measured by bali score - an application provided together with the database. The standard accuracy measures are the Sum of Pairs (SP) and the Total Column (TC). We have found that, for non-core block columns, results calculated by bali score are different from those obtained on the basis of the formal definitions of the measures. ; We do not claim that one of these measures is better than the other, but they are definitely different. Such a situation can be the source of confusion when alignments obtained using various methods are compared. Therefore, we propose a new nomenclature for the measures of the quality of multiple sequence alignments to distinguish which one was actually calculated. Moreover, we have found that the occurrence of a gap in some column in the first sequence of the reference alignment causes column discarding.
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Zielona Góra: Uniwersytet Zielonogórski
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AMCS, volume 19, number 4 (2009) ; click here to follow the link
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Biblioteka Uniwersytetu Zielonogórskiego
Object collections:
- Repository > Faculties > Faculty of Computer, Electrical and Control Engineering
- Repository > Types of work > Articles
- Repository > Scientific journals and UZ publishing series > International Journal of Applied Mathematics and Computer Science (AMCS) > International Journal of Applied Mathematics and Computer Science (AMCS) (2009)
Last modified:
Apr 10, 2024
In our library since:
Apr 10, 2024
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60
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https://zbc.uz.zgora.pl/repozytorium/publication/88595
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International Journal of Applied Mathematics and Computer Science (AMCS)
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International Journal of Applied Mathematics and Computer Science (AMCS), volume 20 (2010)
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International Journal of Applied Mathematics and Computer Science (AMCS), volume 19 (2009)
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| Edition name | Date |
|---|---|
| Some remarks on evaluating the quality of the multiple sequence alignment based on the BAliBASE benchmark | Apr 10, 2024 |
