• Journal of Information Processing Systems
• /
• 제20권4호
• /
• pp.432-441
• /
• 2024

To improve the security of gene information and the accuracy of matching, this paper designs a homomorphic encryption algorithm for gene matching based on cloud computing environment. Firstly, the gene sequences of cloud files entered by users are collected, which are converted into binary code by binary function, so that the encrypted text is obviously different from the original text. After that, the binary code of genes in the database is compared with the generated code to complete gene matching. Experimental analysis indicates that when the number of fragments in a 1 GB gene file is 65, the minimum encryption time of the algorithm is 80.13 ms. Aside from that, the gene matching time and energy consumption of this algorithm are the least, which are 85.69 ms and 237.89 J, respectively.

• 대한전자공학회:학술대회논문집
• /
• 대한전자공학회 1999년도 하계종합학술대회 논문집
• /
• pp.474-478
• /
• 1999

Genetic algorithm is an efficient search method using principles of natural selection and population genetics. In conventional genetic algorithms, however, the size of gene pool should be increased to insure a convergency. Therefore, many memory spaces and much computation time were needed. Also, since child chromosomes were generated by chromosome crossover and gene mutation, the algorithms have a complex structure. Thus, in this paper, a compact stereo matching algorithm using a population-based incremental teaming based on probability vector is proposed to reduce these problems. The PBIL method is modified for matching environment. Since the Proposed algorithm uses a probability vector and eliminates gene pool, chromosome crossover, and gene mutation, the matching algorithm is simple and the computation load is considerably reduced. Even if the characteristics of images are changed, stable outputs are obtained without the modification of the matching algorithm.

• 제어로봇시스템학회논문지
• /
• 제12권10호
• /
• pp.1044-1049
• /
• 2006

Multiple sequence alignment is a method to compare two or more DNA or protein sequences. Most of multiple sequence alignment tools rely on pairwise alignment and Smith-Waterman algorithm to generate an alignment hierarchy. Therefore, in the existing multiple alignment method as the number of sequences increases, the runtime increases exponentially. In order to remedy this problem, we adopted a parallel processing suffix tree algorithm that is able to search for common subsequences at one time without pairwise alignment. Also, the cross-matching subsequences triggering inexact-matching among the searched common subsequences might be produced. So, the cross-matching masking process was suggested in this paper. To identify the function of the clusters generated by suffix tree clustering, BLAST and CDD (Conserved Domain Database)search were combined with a clustering tool. Our clustering and annotating tool consists of constructing suffix tree, overlapping common subsequences, clustering gene sequences and annotating gene clusters by BLAST and CDD search. The system was successfully evaluated with 36 gene sequences in the pentose phosphate pathway, clustering 10 clusters, finding out representative common subsequences, and finally identifying functional domains by searching CDD database.

• 전자공학회논문지S
• /
• 제36S권10호
• /
• pp.103-112
• /
• 1999

유전 알고리즘은 적절한 해를 찾기 위해서 자연선택과 개체군 유전학을 이용한 효율적 탐색기법이다. 그러나, 기존의 유전 알고리즘들은 수렴을 보장하기 위해서 유전자 풀의 크기를 증가시켜야 했고 그 결과 저장공간과 계산 시간이 많이 소요되었다. 또한, 염색체 교차와 유전자 돌연변이를 사용하여 새로운 염색체를 발생시켰기 때문에 알고리즘이 복잡하다는 단점이 있다. 본 논문에서는 이런 문제를 줄이기 위해서 확률벡터에 기반한 개체기반 증가 학습이라는 소형 유전 알고리즘을 정합 환경에 맞게 변형시킨 새로운 스테레오 정합 방법을 제안하였다. 제안된 알고리즘은 확률벡터의 사용으로 인해 유전 풀, 염색체 교차, 그리고 유전자 돌연변이 연산을 제거하였다. 그 결과 제안된 정합 알고리즘은 기존 방식보다 구조가 간단하고 계산량의 향상이 있었으며, 영상의 특성에 상관없이 안정된 결과를 얻을 수 있다는 장점이 있었다.

• 제어로봇시스템학회논문지
• /
• 제11권10호
• /
• pp.851-856
• /
• 2005

The DNA and protein data of diverse species have been daily discovered and deposited in the public archives according to each established format. Database systems in the public archives provide not only an easy-to-use, flexible interface to the public, but also in silico analysis tools of unidentified sequence data. Of such in silico analysis tools, multiple sequence alignment [1] methods relying on pairwise alignment and Smith-Waterman algorithm [2] enable us to identify unknown DNA, protein sequences or phylogenetic relation among several species. However, in the existing multiple alignment method as the number of sequences increases, the runtime increases exponentially. In order to remedy this problem, we adopted a parallel processing suffix tree algorithm that is able to search for common subsequences at one time without pairwise alignment. Also, the cross-matching subsequences triggering inexact-matching among the searched common subsequences might be produced. So, the cross-matching masking process was suggested in this paper. To identify the function of the clusters generated by suffix tree clustering, BLAST was combined with a clustering tool. Our clustering and annotating tool is summarized as the following steps: (1) construction of suffix tree; (2) masking of cross-matching pairs; (3) clustering of gene sequences and (4) annotating gene clusters by BLAST search. The system was successfully evaluated with 22 gene sequences in the pyrubate pathway of bacteria, clustering 7 clusters and finding out representative common subsequences of each cluster

• 컴퓨터교육학회논문지
• /
• 제14권2호
• /
• pp.83-94
• /
• 2011

생의학분야에서 문헌에 표기된 개체를 인식하기 위해 길이우선매칭기법을 빈번히 사용한다. 길이우선매칭기법은 사전을 이용한 개체인식기법으로 좋은 사전만 구축되어 있다면 빠르고 정확하게 개체를 찾아낼 수 있다는 장점을 가진다. 그러나 개체가 나열되고 중복된 단어가 생략될 경우에는 길이우선매칭기법을 이용할 경우 성능이 현저히 떨어지게 된다. 우리는 이러한 인식성능문제를 해결하기 위해 부분매칭기법을 제안한다. 제안된 부분매칭기법은 생략이 발생될 수 있다는 것을 가정하여 다수의 후보개체를 만들어 내고 그 후에 최적화 알고리즘을 통해 다수의 개체후보 중에서 가장 타당해 보이는 개체를 선택한다. 우리는 생의학분야의 개체 중에서 나열되는 경우가 빈번한 HLA 유전자, HLA 항원, HLA 대립유전자 개체들을 대상으로 길이우선매칭기법과 제안된 부분매칭기법의 개체인식성능을 분석하였다. 3종의 HLA 개체들을 인식하기 위해서 먼저 확장사전과 태그기반사전을 구축하였으며, 그 후 구축된 사전을 이용해 길이우선매칭과 부분매칭을 수행하였다. 실험결과에 따르면 길이우선매칭기법은 HLA 항원 개체에서 좋은 성능을 보였으며 부분매칭기법은 생략된 표현이 빈번한 HLA 유전자 개체, HLA 대립유전자 개체에서 좋은 성능을 보였다. 부분매칭기법은 HLA 대립유전자 개체를 대상으로 95.59%의 높은 F-score를 얻었다.

• 정보처리학회논문지B
• /
• 제12B권4호
• /
• pp.429-436
• /
• 2005

본 논문에서는 유전자 알고리즘의 일반적인 문제점인 과도한 저장공간의 소모와 탐색의 비효율성을 줄이기 위해 PBIL을 이용한 단순한 스테레오 정합 기법을 제안한다. PBIL은 확률벡터에 기반해서 통계적 탐색과 경쟁학습을 이용하는 변종 유전자 알고리즘이며 확률벡터의 사용으로 인해 직렬 및 병렬 유전자 알고리즘군에 비해 단순한 구조를 가진다. 본 논문에서는 이 PBIL을 스테레오 정합 환경에 맞게 변형 및 단순화시켜 정합 알고리즘을 개발한다. 높은 적응성을 갖는 염색체는 생존 확률 또한 높다는 진화 법칙을 보존하면서 유전자 풀, 염색체 교차 및 유전자 돌연변이를 제거할 수 있으며 그 결과 저장공간을 줄이고 정합 규칙을 간소화하여 계산 비용을 감소시킬 수 있다. 추가적으로 다해상도 정합 기법처럼 넓은 영역의 변이 일관성을 획득하기 위해 변이 연속성에 대한 이웃들의 거리를 제어하는 방식을 추가하여 고정된 작은 정합창을 사용하면서 안정된 결과를 얻을 수 있게 한다. 마지막으로 단순한 시스템에 적용될 수 있게 하기 위해서 확률벡터를 사용하지 않는 제안한 알고리즘의 소형 대안 기법을 제시한다.

• 대한수의학회지
• /
• 제43권1호
• /
• pp.95-102
• /
• 2003

Because Staphylococcus aureus (S. aureus) has variable number of short sequence repeat region in coagulase gene, it has been used to investigate the relatedness of S. aureus isolates. In this study, we isolated S. aureus strains from 20 dairy farms with bovine mastitis from September 2000 to August 2001. PCR-RFLP analysis of coagulase gene revealed 10 different patterns. Most of the S. aureus isolates showed only one coagulase gene RFLP pattern per farm. However, there were several S. aureus clones spreading between dairy farms. All the farms showed poor management conditions of milking machine and milker, indicating that managements for mastitis control program include use of proper milking matching, premilking sanitation, and segregation in the S. aureus infection herd. Our data suggest that PCR-RFLP analysis of coagulase gene might be applicable for the epidemiological investigations of S. aureus isolated from bovine mastitis cows.

• KSBB Journal
• /
• 제26권2호
• /
• pp.131-138
• /
• 2011

Some computational approaches are needed for clarifying RNAi sequences, because it takes much time and endeavor that almost of RNAi sequences are verified by experimental data. Incorrectness of RNAi mechanism and other unaware factors in organism system are frequently faced with questions regarding potential use of RNAi as therapeutic applications. Our massive parallelized pair alignment scoring between dsRNA in Genebank and expressed sequence tags (ESTs) in Caenorhabditis elegans Genome Sequencing Projects revealed that this provides a useful tool for the prediction of RNAi induced cosuppression details for practical use. This pair alignment scoring method using high performance computing exhibited some possibility that numerous unwanted gene silencing and cosuppression exist even at high matching scores each other. The classifying the relative higher matching score of them based on GO (Gene Ontology) system could present mapping dsRNA of C. elegans and functional roles in an applied system. Our prediction also exhibited that more than 78% of the predicted co-suppressible genes are located in the ribosomal spot of C. elegans.

• Journal of Microbiology and Biotechnology
• /
• 제18권12호
• /
• pp.1953-1957
• /
• 2008

Recombinant Lactobacillus strains have been constructed using gene splicing by overlap extension (SOE). Primers were designed of which one end of an amplified product contained complementary sequences for an end of other amplified fragment. For efficient matching, we used an asymmetric PCR step that was effective at generating an excess of strands that would anneal in the final PCR. CP12, a recombinant fragment consisting of the integrase gene and attachment site of the bacteriophage A2, was constructed and inserted into the genome of Lactobacillus casei ATCC 393, yielding Lb. casei ATCC 393::XCP12. Another recombinant Lb. casei strain was constructed, where the egfp gene was a part of the construction. The EGFP produced from Lb. casei ATCC 393::XCEGFP14 was detected by Western blot hybridization. This simple and widely applicable approach has significant advantages over standard recombinant DNA techniques for Lactobacillus species.