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Some remarks on evaluating the quality of the multiple sequence alignment based on the BALiBASE benchmark

100%
Błażewicz J., Formanowicz P., Wojciechowski P.
International Journal of Applied Mathematics and Computer Science
|
2009
|
tom 19
|
nr 4
675-678
EN
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.
2
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Internet shopping optimization problem

88%
Błażewicz J., Kovalyov M., Musiał J., Urbański A., Wojciechowski A.
International Journal of Applied Mathematics and Computer Science
|
2010
|
tom 20
|
nr 2
385-390
EN
A high number of Internet shops makes it difficult for a customer to review manually all the available offers and select optimal outlets for shopping. A partial solution to the problem is brought by price comparators which produce price rankings from collected offers. However, their possibilities are limited to a comparison of offers for a single product requested by the customer. The issue we investigate in this paper is a multiple-item multiple-shop optimization problem, in which total expenses of a customer to buy a given set of items should be minimized over all available offers. In this paper, the Internet Shopping Optimization Problem (ISOP) is defined in a formal way and a proof of its strong NP-hardness is provided. We also describe polynomial time algorithms for special cases of the problem.
3
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New machine learning methods for prediction of protein secondary structures

75%
Błażewicz J., Łukasik P., Wilk S.
Control and Cybernetics
|
2007
|
tom 36
|
nr 1
183-201
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