• The Journal of the Korea institute of electronic communication sciences
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• v.19 no.2
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• pp.467-472
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• 2024

Multiple sequence alignment (MSA) is a method of collecting and aligning multiple protein sequences or nucleic acid sequences that perform the same function in various organisms at once. clustalW, a representative multiple sequence alignment algorithm using BioPython, compares the degree of alignment by column position. In addition, a web logo and phylogenetic tree are created to visualize conserved sequences in order to improve understanding. An example was given to confirm the differences between humans and other species, and applications of BioPython are presented.

• Bioinformatics and Biosystems
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• v.1 no.1
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• pp.82-87
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• 2006

The most popular protein structure prediction method is comparative modeling. To guarantee accurate comparative modeling, the sequence alignment between a query protein and a template should be accurate. Although choosing the best template based on the protein sequence alignments is most critical to perform more accurate fold-recognition in comparative modeling, even more critical is the sequence alignment quality. Contrast to a lot of attention to developing a method for choosing the best template, prediction of alignment accuracy has not gained much interest. Here, we develop a method for prediction of the shift score, a recently proposed measure for alignment quality. We apply support vector regression (SVR) to predict shift score. The alignment between a query protein and a template protein of length n in our own library is transformed into an input vector of length n +2. Structural alignments are assumed to be the best alignment, and SVR is trained to predict the shift score between structural alignment and profile-profile alignment of a query protein to a template protein. The performance is assessed by Pearson correlation coefficient. The trained SVR predicts shift score with the correlation between observed and predicted shift score of 0.80.

• The KIPS Transactions:PartC
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• v.14C no.5
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• pp.411-416
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• 2007

The General security method of wireless network provides a confidentiality of communication contents based on the cryptographic stability against a malicious host. However, this method exposes the logical and physical addresses of both sender and receiver, so transmission volume and identification of both may be exposed although concealing that content. Covered address scheme that this paper proposes generates an address to which knapsack problem using super increasing sequence is applied, and replaces the addresses of sender and receiver with addresses from super increasing sequence. Also, proposed method changes frequently secret addresses, so a malicious user cannot watch a target system or try to attack the specific host. Proposed method also changes continuously a host address that attacker takes aim at. Accordingly, an attacker who tries to use DDoS attack cannot decide the specific target system.

• 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 KIISE
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• v.43 no.10
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• pp.1067-1072
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• 2016

Software birthmarks, which are unique characteristics of the software, are used to detect software plagiarism or software similarity. Generally, software birthmarks are divided into static birthmarks or dynamic birthmarks, which have evident pros and cons depending on the extraction method. In this paper, we propose a method for extracting the API sequence birthmarks using a dynamic analysis and similarity detection between the executable codes. Dynamic birthmarks based on API sequences extract API functions during the execution of programs. The extracted API sequences often include all the API functions called from the start to the end of the program. Meanwhile, our dynamic birthmark scheme extracts the API functions only called directly from the executable code. Then, it uses a sequence alignment algorithm to calculate the similarity metric effectively. We evaluate the birthmark with several open source software programs to verify its reliability and credibility. Our dynamic birthmark scheme based on the extracted API sequence can be utilized in a similarity test of executable codes.

• The Journal of the Acoustical Society of Korea
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• v.40 no.4
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• pp.370-381
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• 2021

This paper presented an efficient transceiver structure of multiband Frequency Shift Keying (FSK) signals with direct sequence spread spectrum for maintaining covertness and performance. In aspect to covertness, direct sequence spread spectrum method, which multiplying by Pseudo Noise (PN) codes whose rate is much higher than that of data sequence, is employed. In aspect to performance, in order to overcome performance degradation caused by multipath and Doppler spreading, we applied multiband, turbo equalization, and weighting algorithm are applied. Based on the simulation results, by applying 4 number of multiband and number of chips are 8 and 32, experiments were conducted in a lake with a distance of moving from 300 m to 500 m between the transceivers. we confirmed that the performance was improved as the number of bands and chips are increased. Furthermore, the performance of multiband was improved when the proposed weighting algorithm was applied.

• Journal of KIISE:Databases
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• v.35 no.4
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• pp.356-367
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• 2008

As XML is gaining unqualified success in being adopted as a universal data representation and exchange format, particularly in the World Wide Web, the problem of querying XML documents poses interesting challenges to database researcher. Several structural XML query processing methods, including XISS and XR-tree, for past years, have been proposed for fast query processing. However, structural XML query processing has the problem of requiring expensive Join cost for twig path query Recently, sequence matching based XML query processing methods, including ViST and PRIX, have been proposed to solve the problem of structural XML query processing methods. Through sequence matching based XML query processing methods match structured queries against structured data as a whole without breaking down the queries into sub queries of paths or nodes and relying on join operations to combine their results. However, determining the structural relationship of ViST is incorrect because its numbering scheme is not optimized. And PRIX requires many processing time for matching LPS and NPS about XML data trees and queries. Therefore, in this paper, we propose efficient sequence matching method u sing the bottom-up query processing for efficient XML query processing. Also, to verify the superiority of our index structure, we compare our sequence matching method with ViST and PRIX in terms of query processing with linear path or twig path including wild-card('*' and '//').

• The KIPS Transactions:PartD
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• v.13D no.7 s.110
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• pp.923-930
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• 2006

In this paper we design the system test model for the weapon system embedded software based on the Time Factor Method(TFM) considering time factors and suggest the results through the case study. For doing this, we discuss the features, system tests and the object-oriented model based UML notations of the weapon system embedded software. And we give a test method considering time factors, a measuring method to time factors, and a test case selection algorithm as an approach to the TFM for designing the system test model. The TFM based system test model consists of three factors (X, Y, Z) in the weapon system embedded software. With this model, we can extract test cases through the selection algorithm for a maximum time path in 'X', identify the objects related to the Sequence Diagram in 'Y' and measure the execution time of each objects which is identified by the Timing Diagram in 'Z' Also, we present the method of extracting the system test cases by applying the proposed system test model to the 'Multi-function missile defense system'.

• The Journal of Korea Robotics Society
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• v.10 no.2
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• pp.96-103
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• 2015

In this paper, we first point out the limitation of the existing methods in usability evaluation, and propose a new method to find tasks and users that can cause problems in the use of software applications. To deal with object-based applications, we define unit actions and divide a given task into the sequence of unit actions. Then, we propose a new measure to calculate the degree of lostness for the unit actions. In several experiments, we show the proposed method can represent the usability well while the previous method has a problem in object-based applications. We also find that the user's evaluation is more related to the proposed method than the previous method based on execution time through correlation analysis.

• Journal of the Institute of Electronics and Information Engineers
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• v.51 no.2
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• pp.95-101
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• 2014

This paper explains effective tracking method for a vehicle cutting in a line on the road automatically. The method employs KLT based on optical flow using play-back image sequence. Main contribution of this paper is play-back image sequence that is in order image frames for rewind direction from a reference point in time. The moment when recognizing camera can read a license plate very well can usually be the reference point in time. The biggest images of object traced can usually be obtained at this moment also. When optic flow is applied, the bigger image of the object traced can be obtained, the more feature points can be obtained. More many feature points bring good result of tracking object. After the recognizing cameras read a license plate on the vehicle suspected of cut-in-line violation, and then the system extracts the play-back image sequence from the tracking cameras for watching wide range. This paper compares using play-back image sequence as normal method for tracking to using play-forward image sequence as suggested method on the results of the experiment and also shows the suggested algorithm has a good performance that can be applied to the unmanned system for watching cut-in-line violation.