• The Journal of the Convergence on Culture Technology
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• v.5 no.3
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• pp.339-344
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• 2019

Global sequence alignment in search of similarity or homology favors larger size of the sequence because it keeps looking for more similar section between two sequences in the hope that it adds up scores for matched part in the rest of the sequence. If a substantial size of mismatched section exists in the middle of the sequence, it greatly reduces the total alignment score. In this case a whole sequence would be better to be divided into multiple sections. Overall alignment score over the multiple sections of the sequence would increase as compared to global alignment. This method is called multiple local alignment. In this paper, we implement a multiple local alignment algorithm, an extension of Smith-Waterman algorithm and show the experimental results for the algorithm that is able to search for sub-optimal sequence.

• Proceedings of the Korea Information Processing Society Conference
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• 2003.05b
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• pp.1019-1022
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• 2003

두 서열을 비교하여 유사성(similarity)이나 상동성(homology)를 찾기 위한 서열 정렬 방법 중에서 지역 정렬에 많이 사용되는 Smith-Waterman 알고리즘의 제한점인 Mosaic effect와 Shadow effect를 극복하기 위한 효율적인 방법을 살펴보고, 하나의 최대 값이 아닌 다수개의 최대 값을 찾아 다수개를 정렬함으로써 서열내에 존재 할 수 있는 다수개의 지역 정렬을 찾고 Normalized sequence alignment 알고리즘을 이용하여 서열 정렬된 결과들의 우선 순위를 매겨본다.

• Journal of the Korean Data and Information Science Society
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• v.17 no.4
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• pp.1289-1297
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• 2006

Before other statistical data analysis the preprocessing steps should be performed adequately to have meaningful results. These steps include processes such as baseline correction, normalization, denoising, and multiple alignment. In this paper an algorithm for baseline correction is proposed with using the piecewise cubic Hermite interpolation with block-selected points and local minima after denoising for SELDI or MALDI mass spectrometry data.

• Proceedings of the Korea Information Processing Society Conference
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• 2002.11c
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• pp.2337-2340
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• 2002

본 연구는 생물정보학(Bioinformatics)의 가장 기초적인 분야중 하나인, 새롭게 밝혀진 유전자 서열과 이미 밝혀진 유전자 서열 사이의 유사성(similarity)이나 상동성(homology)을 찾기 위한 방법에 대한 연구 중 지역 서열정렬로 사용하는 알고리즘인 Smith-Waterman 알고리즘이 갖고 있는 문제를 파악한다. 긴 서열에 대한 선호를 막고 대신 부분적인 지역 정렬을 다수 개 찾아 정렬시키는 알고리즘을 제안하기로 한다.

• The Journal of the Korea Contents Association
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• v.16 no.10
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• pp.608-616
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• 2016

The Smith-Watrman (SW) algorithm is a local alignment algorithm which is one of important operations in DNA sequence analysis. The SW algorithm finds the optimal local alignment with respect to the scoring system being used, but it has a problem to demand long execution time. To solve the problem of SW, some methods to perform SW in distributed and parallel manner have been proposed. The ADAM which is a distributed and parallel processing framework for DNA sequence has parallel SW. However, the parallel SW of the ADAM does not consider that the SW is a dynamic programming method, so the parallel SW of the ADAM has the limit of its performance. In this paper, we propose a method to enhance the parallel SW of ADAM. The proposed parallel SW (PSW) is performed in two phases. In the first phase, the PSW splits a DNA sequence into the number of partitions and assigns them to multiple nodes. Then, the original Smith-Waterman algorithm is performed in parallel at each node. In the second phase, the PSW estimates the portion of data sequence that should be recalculated, and the recalculation is performed on the portions in parallel at each node. In the experiment, we compare the proposed PSW to the parallel SW of the ADAM to show the superiority of the PSW.

• The Journal of Korean Physical Therapy
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• v.15 no.4
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• pp.412-430
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• 2003

Functional stability is dependent on integrated local and global muscle function. Movement dysfunction can present as a local and global problem, though both frequently occur together. To good understand how movement induces pain syndrome, the optimal actions and interaction of the multiple anatomic and functional systems involved in motion must be considered. Minor alterations in the precision of movement cause microtrauma and, if allowed to continue, will cause macrotrauma and pain. These alteration of the movement result in the development of compensatory movement and movement impairment. Muscle that become tight tend to pull the body segment to which they are attached, creating postural deviation. The antagonistic muscles may become weak and allow postural deviations due to lack of balanced support. Both hypertonic and inhibited muscles will cause an alteration of the distribution of pressure over the joint(s) that they cross and, thus, may not only result from muscle dysfunction, but produce joint dysfunction as well. Alteration of the shoulder posture and movement dysfunction may sometimes result in compression of neurovascular structures in the shoulder and arm. There is a clear link between reduced proprioceptive input, altered motor unit recruitment and the neurovascular compression. This report start with understanding of the impaired alignment, movement patterns and neuromuscular compression of the shoulder girdle by movement impairment to approach method of the movement dysfunction.

• Interdisciplinary Bio Central
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• v.3 no.4
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• pp.14.1-14.9
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• 2011

Protein homology detection is an important issue in comparative genomics. Because of the exponential growth of sequence databases, fast and efficient homology detection tools are urgently needed. Currently, for homology detection, sequence comparison methods using local alignment such as BLAST are generally used as they give a reasonable measure for sequence similarity. However, these methods have drawbacks in offering overall sequence similarity, especially in dealing with eukaryotic genomes that often contain many insertions and duplications on sequences. Also these methods do not provide the explicit models for speciation, thus it is difficult to interpret their similarity measure into homology detection. Here, we present a novel method based on Word Conservation Score (WCS) to address the current limitations of homology detection. Instead of counting each amino acid, we adopted the concept of 'Word' to compare sequences. WCS measures overall sequence similarity by comparing word contents, which is much faster than BLAST comparisons. Furthermore, evolutionary distance between homologous sequences could be measured by WCS. Therefore, we expect that sequence comparison with WCS is useful for the multiple-species-comparisons of large genomes. In the performance comparisons on protein structural classifications, our method showed a considerable improvement over BLAST. Our method found bigger micro-syntenic blocks which consist of orthologs with conserved gene order. By testing on various datasets, we showed that WCS gives faster and better overall similarity measure compared to BLAST.

• Journal of Microbiology and Biotechnology
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• v.28 no.4
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• pp.622-629
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• 2018

Expansins are cell wall proteins that mediate cell wall loosening and promote specific tissue and organ morphogenesis in plants and in some microorganisms. Unlike plant expansins, the biological functions of fungal expansin-like proteins have rarely been discussed. In the present study, an expansin-like protein-encoding fvexpl1 gene, was identified from Flammulina velutipes by using local BLAST. It consisted of five exons with a total length of 822 bp. The deduced protein FVEXPL1 contained 274 amino acids with a predicted molecular mass and isoelectric point of 28,589 Da and pH 4.93, respectively. The first 19 amino acids from the N terminal are the signal peptide. Phylogenetic analysis and multiple protein alignment indicated FVEXPL1 was an expansin-like protein. The expression level of fvexpl1 gene in the stipe was significantly higher than that in the mycelia, primordia, and cap. However, the expression level of fvexpl1 gene was significantly higher in the fast elongation region of the stipe as compared with the slow elongation region. Expression analysis indicated that fvexpl1 gene might have an auxiliary role in the stipe morphogenesis of F. velutipes.

• Journal of Korea Port Economic Association
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• v.30 no.3
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• pp.163-185
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• 2014

The growth of a city requires substantial resources, an appropriate environment, and the alignment of several factors. City growth also evolves through changes in its history, culture, economics, societies, groups, and government systems. However, current port city development plans designed to encourage the growth of local businesses fail to provide the support needed for both the city and businesses. The recent actions of urban administrations and federal and local governments have revealed that they have yet to create a mature decentralized management system, or perhaps have ignored the reality of needing one. Taking a clear look at the differences between port regions, such as Gwangyang and Pyeongtaek, and understanding their effect on city growth would be a prudent course of action when preparing for future developments. The purpose of this study is to determine the relationship between ports and cities by analyzing the effect of port characteristics on nearby city growth. This study used a comparison analysis to determine how port characteristics affected the growth of Pyeongtaek and Gwangyang. One result of this analysis showed that an increase in the number of goods being imported or exported had a positive effect on the growth of both port cities, In this respect, an aggressive plan and cooperation between the federal and local government should occur simultaneously. Furthermore, efficient local policies that focus on the increase of personnel and material resources should be pursued as a standard strategy, which would also promote the international status of these locations. The results of this study show the importance of government cooperation. The federal government should lead with aggressive strategies that aim to optimize efficiency, while the local government should provide the necessary assistance and coordination in order to achieve optimal results.