Wyniki wyszukiwania - BazTech

1

Keram: a novel stand-alone application for correlated mutations identification and analysis

Kuśka J., Leluk J., Lesyng B.

Bio-Algorithms and Med-Systems

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2011

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Vol. 7, no. 1

71--76

EN

Keram is a stand-alone Windows 2000/XP/Vista application designed for the detection and analysis of the correlated mutations. Study of this phenomenon provides important information about protein structure stability factors as well as the formation of protein complexes. It is generally assumed that the mechanism of compensation explains the mutations that occur simultaneously. Keram is designed to detect the mutational correlations by comparative analysis of multiple sequence alignments. Additionally a three dimensional structure can be applied to calculate the distance between correlated positions in the protein molecule. Keram has been succesfully applied for the analysis of kinase subfamilies. The obtained data suggest that the mechanism of compensation does not explain utterly this phenomenon which seems to be much more complex and diverse. The residues that are detected as correlated are often placed at very distant positions of the protein structure, therefore the direct mutual interaction between them is impossible. We have detected not only correlated pairs, but also clusters of positions (even more than 10) that reveal correlated changeability.

2

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

Błażewicz J., Formanowicz P., Wojciechowski P.

International Journal of Applied Mathematics and Computer Science

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2009

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Vol. 19, no 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.

3

Multisequence Alignment as a new tool for network traffic analysis

Fabjański K., Kozakiewicz A., Felkner A., Kijewski P., Kruk T.

Prace Naukowe Politechniki Warszawskiej. Elektronika

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2007

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z. 160

59-70

EN

This article presents a multiple sequence alignment as a method used for problems of motif finding [13] in network traffic collection. Based on multisequence alignment we will present two bioinformatics approaches for finding longest common subsequence (LCS) [14] of network traffic signatures collection. the article starts from presenting the description of pairwise alignment algorithms, goes through the examples of its implementation and then comes to the part related to bioinformatics methods. At the end, some preliminary results concerning Center Star method will be presented.

4

Clustal W algorithm for multiple sequence alignment revisited

Błażewicz J., Formanowicz P., Kasprzak M., Michalak K., Wierzejewski P.

Foundations of Computing and Decision Sciences

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2001

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Vol. 26, No. 3

189-196

EN

Multiple sequence alignment is one of the most important problems arising in DNA and protein recognition. Clustal W is a well known and practically [ applied method used for solving the problem. In the paper, a modification of the algorithm is described which shortens considerably its mean running time. The modification uses graphs of partial alignments and operations on resulting semi-cliques. As shown by an extensive computational experiment running time is reduced up to 50%, as compared with the original approach.