Autor:
Błażewicz, Jacek ; Formanowicz, Piotr ; Wojciechowski, Paweł
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Temat i słowa kluczowe:
multiple sequence alignment ; reference alignment ; alignment accuracy
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.
Wydawca:
Zielona Góra: Uniwersytet Zielonogórski
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Źródło:
AMCS, volume 19, number 4 (2009) ; kliknij tutaj, żeby przejść