• International Journal of Contents
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• v.14 no.1
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• pp.34-38
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• 2018

With the rapid growth of genomic data, new requirements have emerged that are difficult to handle with big data storage and analysis techniques. Regardless of the size of an organization performing genomic data analysis, it is becoming increasingly difficult for an institution to build a computing environment for storing and analyzing genomic data. Recently, cloud computing has emerged as a computing environment that meets these new requirements. In this paper, we analyze and compare existing distributed and parallel NGS (Next Generation Sequencing) analysis based on cloud computing environment for future research.

• 한국생물공학회:학술대회논문집
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• 2002.04a
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• pp.539-542
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• 2002

We propose new encoding method for numerical data in DNA using temperature gradient. To represent numerical values in DNA sequences, we introduce melting temperature. Since DNA strands representing smaller values have a lower Tm, they tend to denature with ease and also easily amplified by denaturation temperature gradient PCR. We also implement a local search molecular algorithm using temperature gradient, which is contrasted to conventional exhaustive search molecular algorithms. The proposed methods are verified by solving an instance of the travelling salesman problem. We could effectively amplify the correct solutions and the use of temperature gradient made the detection of solutions easier.

• Proceedings of the KIEE Conference
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• 1996.07b
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• pp.1368-1370
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• 1996

The Information of Edges which takes small area comparing with the total image is very important in DNA images as well as general images. DNA image is the object should be managed by computing and it's demanding information is less than general images, but the accuracy is more important In a huge DNA image processing system such as DNA Information Bank, the performance depends on the size of image. In this paper, we extract the edge information and make it as a binary image. To reduce the size of the original image, it was applied by JPEG image compression method. The compressed image is combined with edge information when they are restored. As a result, Both the image compression ratio and restoration quality are optimized without the loss of critical information.

• Journal of KIISE:Computing Practices and Letters
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• v.16 no.3
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• pp.275-280
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• 2010

A local alignment algorithm finds a substring pair of given two strings where two substrings of the pair are similar to each other. A DNA sequence can consist of not only A, C, G, and T but also N and X where N and X are used when the original bases lose their information for various reasons. In this paper, we present an efficient local alignment algorithm for two DNA sequences including N and X using the affine gap penalty metric. Our algorithm is an extended version of the Kim-Park algorithm and can be extended in case of including other characters which have similar properties to N and X.

• Journal of Internet Computing and Services
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• v.19 no.2
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• pp.1-7
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• 2018

Due to advances in DNA sequencing technologies, its medical value continues to grow. However, once genome data leaked, it cannot be revoked, and disclosure of personal genome information impacts a large group of individuals. Therefore, secure techniques for managing genomic big data should be developed. We first propose a privacy-preserving inner product protocol for large data sets using the homomorphic encryption of Gentry et al., and then we introduce an efficient privacy-preserving DNA matching protocol based on the proposed protocol. Our efficient protocol satisfies the requirements of correctness, confidentiality, and privacy.

• The Journal of the Korea Contents Association
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• v.10 no.7
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• pp.81-87
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• 2010

This paper proposes a G-BLAST(BLAST using Grid Computing) system, an integrated software package for BLAST searches operated in heterogeneous distributed environment. G-BLAST employed 'database splicing' method to improve the performance of BLAST searches using exists computing resources. G-BLAST is a basic local alignment search tool of DNA Sequence using grid computing in heterogeneous distributed environment. The G-BLAST improved the existing BLAST search performance in gene sequence analysis. Also G-BLAST implemented the pipeline and data management method for users to easily manage and analyze the BLAST search results. The proposed G-BLAST system has been confirmed the speed and efficiency of BLAST search performance in heterogeneous distributed computing.

• Journal of the Institute of Electronics and Information Engineers
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• v.52 no.11
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• pp.66-78
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• 2015

With the development of bio computing technology, DNA watermarking to do as a medium of DNA information has been researched in the latest time. However, DNA information is very important in biologic function unlikely multimedia data. Therefore, the reversible DNA watermarking is required for the host DNA information to be perfectively recovered. This paper presents a reversible DNA watermarking using least square based prediction error expansion for noncodng DNA sequence. Our method has three features. The first thing is to encode the character string (A,T,C,G) of nucleotide bases in noncoding region to integer code values by grouping n nucleotide bases. The second thing is to expand the prediction error based on least square (LS) as much as the expandable bits. The last thing is to prevent the false start codon using the comparison searching of adjacent watermarked code values. Experimental results verified that our method has more high embedding capacity than conventional methods and mean prediction method and also makes the prevention of false start codon and the preservation of amino acids.

• Proceedings of the Korea Information Processing Society Conference
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• 2001.10b
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• pp.1151-1154
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• 2001

외판원 문제(Traveling Salesman Problem)는 주어진 n개의 도시들과 그 도시들간의 거리비용이 주어졌을 때, 모든 도시들을 정확히 한번씩만 방문하면서 걸린 비용이 최소가 드는 경로를 찾는 문제로 최적해(optimal)을 구하는 것은 전형적인 NP-완전 문제중의 하나이다. 따라서 외판원 문제를 해결하는 다양한 알고리즘들이 개발되고 있다. 특히 요즈음은 실제 생체 분자(bio-molecule)를 계산의 도구로 사용하는 새로운 계산 방법인 DNA 컴퓨팅은 DNA 분자가 잠재적으로 가지고 있는 막대한 병렬성을 이용해서 NP-완전 문제들을 해결하고자 하는 연구들이 땀이 진행되고 있다. 그러나 아직 실제 생체 분자의 특성을 잘 반영하는 계산 모델이나 분자 생물학에서 사용하는 연산들이 많이 개발되지 알아 계산 효율이 비교적 좋지 않다. 따라서 본 논문에서는 외판원 문제를 해결하기 위한 DAN컴퓨팅의 새로운 중합 효소 연쇄 반응(Polymerase Chain Reaction, PCR) 연산을 개발하였다.

• Proceedings of the Korean Information Science Society Conference
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• 2011.06c
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• pp.202-205
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• 2011

본 논문은 DNA 특성분석 기능을 수행하는 전기영동 장치와 분석결과 해석 기능을 수행하는 젤닥 장치를 통합한 장치를 제안하였다. 이들 두 기능을 독립적으로 수행하는 기존의 시스템은 바이오 전문가의 중간 개입 작업이 필요하며 경험치에 의존하는 검사의 부적황성, 높은 오염가능성, 긴 검사시간 등의 한계점을 가지고 있다. 기존 장비에서 독립적으로 수행하던 두 기능을 동시에 수행하도록 하여, 현 시스템의 한계점들을 개선 할 수 있는 장치를 제안하고 구현하였다. 한편 기존에는 완료된 최종 결과 영상 한 장만을 획득 할 수 있었던 것에 반해 특성분석 중에 결과 영상을 실시간으로 모니터링할 수 있어서 DNA 특성 분석의 성공 여부를 조기에 판단할 수 있었다.

• Proceedings of the Korean Information Science Society Conference
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• 2003.10a
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• pp.67-69
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• 2003

바이오네트웍 모델링은 유전자네트웍, 단백질네트웍, 대사회로, 신호전달회로네트웍등에 대하여 각 요소간의 관계를 그래프이론을 통하여 표현하는 작업을 말한다. 특히 조절네트웍의 모델링은 다양한 생물학적 실험 데이터로부터 단백질들간의 활성과 불활성 관계를 유추해내는 것을 말한다. 현재 조절네트웍 모델링을 위한 다양한 알고리즘들이 개발되어 있으나 응용적인 측면에서 유추된 네트웍은 활용성이 부족하다. 본 논문에서는 In Vitro상에서 DNA 컴퓨팅을 이용하여 간단한 연산을 수행함으로서 유전자 조절 기전을 모델링하고자 한다. 이러한 방법의 장점은 DNA컴퓨팅의 연산이 세포의 현재 또는 다음 상태를 In Vivo 상에서 구현되어 진단 등의 문제에 응용될 수 있다는 가능성을 제시해 준다는 것이다.