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.
Zielona Góra: Uniwersytet Zielonogórski
AMCS, volume 19, number 4 (2009) ; kliknij tutaj, żeby przejść
Biblioteka Uniwersytetu Zielonogórskiego
2024-04-10
2024-04-10
42
https://zbc.uz.zgora.pl/publication/88595
Nazwa wydania | Data |
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Some remarks on evaluating the quality of the multiple sequence alignment based on the BAliBASE benchmark | 2024-04-10 |
Formanowicz, Piotr Tanaś, Krzysztof Korbicz, Józef - red. Uciński, Dariusz - red.
Błażewicz, Jacek Kovalyov, Y. Mikhail Musiał, Jędrzej Urbański, Andrzej P. Wojciechowski, Adam Korbicz, Józef - red. Uciński, Dariusz - red.
Zok, Tomasz Antczak, Maciej Riedel, Martin Nebel, David Villmann, Thomas Lukasiak, Piotr Blazewicz, Jacek Szachniuk, Marta Byrski, Aleksander - ed. Kisiel-Dorohinicki, Marek - ed. Dobrowolski, Grzegorz - ed.
Lopez-Loces, Mario C. Musiał, Jędrzej Pecero, Johnatan E. Fraire-Huacuja, Hector J. Blazewicz, Jacek Bouvry, Pascal Korbicz, Józef - red. Uciński, Dariusz - red.