• Bioinformatics and Biosystems
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• v.2 no.1
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• pp.7-11
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• 2007

Methods for making scoring matrix based on phylogenetic tree for all possible exchanges of one amino acid with another. PFMT(Phylogenetic focused Mutation Tendency) matrix is different BLOSUM62 and PAM160 which are the most used scoring matrixes. This matrix calculates possibility of substitution from common ancestor to high spices. PFMT matrix scores substitution frequency in COGs databases which contain 152 KOGs's dataset. PFMT matrix usefully is able to compare between query sequence and sequences of more higher species and show detailed substitution relation of 20 amino acids.

• Interdisciplinary Bio Central
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• v.6 no.4
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• pp.3.1-3.10
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• 2014

Amino acid substitution matrices are essential tools for protein sequence analysis, homology sequence search in protein databases and multiple sequence alignment. The PAM matrix was the first widely used amino acid substitution matrix. The BLOSUM series then succeeded the PAM matrix. Most substitution matrixes were developed by using the statistical frequency of substitution between each amino acid at blocks representing groups of protein families or related proteins. However, substitution of amino acids is based on the similarity of physiochemical properties of each amino acid. In this study, a new approach was used to obtain major physiochemical properties in multiple sequence alignment. Frequency of amino acid substitution in multiple sequence alignment database and selected attributes of amino acids in physiochemical properties database were merged. This merged data showed the major physiochemical properties through principle components analysis. Using factor analysis, these four principle components were interpreted as flexibility of electronic movement, polarity, negative charge and structural flexibility. Applying these four components, BAPS was constructed and validated for accuracy. When comparing receiver operated characteristic ($ROC_{50}$) values, BAPS scored slightly lower than BLOSUM and PAM. However, when evaluating for accuracy by comparing results from multiple sequence alignment with the structural alignment results of two test data sets with known three-dimensional structure in the homologous structure alignment database, the result of the test for BAPS was comparatively equivalent or better than results for prior matrices including PAM, Gonnet, Identity and Genetic code matrix.

• Journal of KIISE:Software and Applications
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• v.34 no.7
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• pp.595-602
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• 2007

This paper proposes a method that discriminates signal peptide and predicts the cleavage site of the secretory proteins cleaved by the signal peptidase I. The preprocessing stage uses hydrophobicity scales of amino acids in order to predict the presence of signal sequence and the cleavage site. The preprocessing enhances the performance of the prediction method by eliminating the non-secretory proteins in the early stage of prediction. for the effective use of support vector machine for the signal sequence prediction, the biologically relevant distance between the amino acid sequences is defined by using the hydrophobicity and substitution matrix; the hydrophobicity can be used to Predict the location of amino acid in a cell and the substitution matrix represents the evolutionary relationships of amino acids. The proposed method showed 98.9% discrimination rates from signal sequences and 88% correct rate of the cleavage site prediction on Swiss-Prot release 50 protein database using the 5-fold-cross-validation. In the comparison tests, the proposed method has performed significantly better than other prediction methods.

• Journal of the Korea Institute of Information Security & Cryptology
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• v.18 no.4
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• pp.53-68
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• 2008

We study on the practical privacy-preserving techniques by matrix-based randomization approach. We clearly examine the relationship between the two parameters associated with the measure of privacy breach and the condition number of matrix in order to achieve the optimal transition matrix. We propose a simple formula for efficiently calculating the inverse of transition matrix which are needed in the re-construction process of random substitution algorithm, and deduce some useful connections among standard error and another parameters by obtaining condition numbers according to norms of matrix and the expectation and variance of the transformed data. Moreover we give some experimental results about our theoretical expressions by implementing random substitution algorithm.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.18 no.8
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• pp.361-366
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• 2017

For two given logical expressions and, when expression contains the same part of the logical expression as expression, substituting for that part of expression is called a substituted logic expression. If a substituted relation is established between the logical expressions, there is an advantage in that the number of literals used in the whole logical expression can be greatly reduced. However, if the substituted relation is not established, there is no simplification effect obtained from the substituted expression. Previous methods proposed a way to find substituted relations between logical expressions for the given logical expressions themselves, and to calculate substituted expressions if only substitution is possible. In this paper, a new method for performing substitution with addition and revision of logic terms is proposed in order to perform substitution, even though there is no substituted relation between two logic expressions. The proposed method is efficiently implemented using a matrix that finds terms to be added. Then, by covering the matrix that has added terms, substituted logic expressions are found. Experiment results show that the proposed method for several benchmark circuits can reduce the number of literals, compared to existing synthesis tools.

• Phonetics and Speech Sciences
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• v.5 no.1
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• pp.47-54
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• 2013

The aim of this study was to analyze consonant articulation errors produced by 90 speakers with cerebral palsy (CP). Phonetic transcriptions were made for 37 single-word utterances containing 70 phonemes: 48 initial consonants and 22 final consonants. Errors of substitution, omission, and distortion were analyzed using a confusion matrix paradigm showing the visualization of error patterns. Results showed that substitution errors in initial and final consonants were most frequent, followed by omission and distortion. Consonant omission occurred more frequently on final consonants. In both initial and final consonants, the within-place errors were more prominent than the within-manner errors. The current results suggest that consonant confusion matrices for dysarthric speech may provide useful information for evaluating speech intelligibility and developing automatic speech recognition system of adults with CP associated dysarthria.

• Proceedings of the KIEE Conference
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• 2000.07a
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• pp.274-275
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• 2000

This paper introduces new ordering algorithms using the graph of data structure and forward/backward substitution of LU decomposition using recursive function. The performance of the algorithm is compared with Tinney's algorithm using 14 bus systems. Test results show that the new fill-in element of Jacobian matrix using the proposed ordering algorithm is same as that of Tinner scheme 3 and the forward/backward substitution can reduce the computation time

• Journal of the Korea Institute of Information and Communication Engineering
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• v.7 no.7
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• pp.1462-1470
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• 2003

According to the necessity about information security as well as the advance of IT system and the spread of the Internet, a variety of cryptography algorithms are being developed and put to practical use. In addition the technique about cryptography attack also is advanced, and the algorithms which are strong against its attack are being studied. If the linear transformation matrix in the block cipher algorithm such as Substitution Permutation Networks(SPN) produces the Maximum Distance Separable(MDS) code, it has strong characteristics against the differential attack and linear attack. In this paper, we propose a new algorithm which cm estimate that the linear transformation matrix produces the MDS code. The elements of input code of linear transformation matrix over GF$({2_n})$ can be interpreted as variables. One of variables is transformed as an algebraic formula with the other variables, with applying the formula to the matrix the variables are eliminated one by one. If the number of variables is 1 and the all of coefficient of variable is non zero, then the linear transformation matrix produces the MDS code. The proposed algorithm reduces the calculation time greatly by diminishing the number of multiply and reciprocal operation compared with the conventional algorithm which is designed to know whether the every square submatrix is nonsingular.

• Proceedings of the Korean Institute of Building Construction Conference
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• 2022.04a
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• pp.164-165
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• 2022

In order to solve problems such as acceleration of resource use and environmental pollution, experiments were conducted with the aim of producing indoor finishing materials that can adsorb fine dust and carbon dioxide using gelite and polymer, which are porous materials. Based on the previous experiment, gelite was substituted at each level in a matrix having a polymer S738P substitution rate of 12.5%, and the results are as follows. As the substitution rate of gelite increased, the amount of fine dust and carbon dioxide adsorption increased, which is believed to be due to physical adsorption due to the high porosity of gelite. However, further experiments are needed as the overall adsorption amount is not high due to the filling inside the matrix due to the polymer.

• Journal of Photoscience
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• v.10 no.1
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• pp.165-173
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• 2003

m-Phenylene-linked biscarbenes, bisnitrenes and carbenonitrenes can be formed photochemically from appropriate nitrogenous precursors. Generation of such reactive intermediates under matrix-isolation conditions allows for their characterization by spectroscopic techniques such as ESR, UV /vis and IR. The latter method is also useful in characterizing secondary products derived from these reactive intermediates. Computational chemistry methods complement experimental IR data, aiding, thus, in identification of such compounds. In addition electronic structure calculations help in developing qualitative and semi-quantitative models, which can be useful in predicting ground-state multiplicities. The parent systems of m-phenylene-linked carbenes and nitrenes have high-spin ground states, but a switching to lower multiplicity can be achieved by chemical substitution. The ground state and various low-lying excited states of m-phenylenecarbenonitrenes can be reasonably approximated by simple valence-bond depictions. Finally, m-phenylenecarbenonitrenes are photoreactive in the inert matrix isomerizing to cyclopropene derivatives.