• Journal of Korea Society of Industrial Information Systems
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• v.17 no.6
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• pp.59-72
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• 2012

Since a protein displays its specific functions when disorder region of protein sequence transits to order region with provoking a biological reaction, the separation of disorder region and order region from the sequence data is urgently necessary for predicting three dimensional structure and characteristics of the protein. To classify the disorder and order region efficiently, this paper proposes a classification/prediction method using sequence data while acquiring a non-biased result on a specific characteristics of protein and improving the classification speed. The emerging patterns based EPs-TFP methods utilizes only the essential emerging pattern in which the redundant emerging patterns are removed. This classification method finds the sequence patterns of disorder region, such sequence patterns are frequently shown in disorder region but relatively not frequently in the order region. We expand P-tree and T-tree conceptualized TFP method into a classification/prediction method in order to improve the performance of the proposed algorithm. We used Disprot 4.9 and CASP 7 data to evaluate EPs-TFP technique, the results of order/disorder classification show sensitivity 73.6, specificity 69.51 and accuracy 74.2.

• Proceedings of the Korea Information Processing Society Conference
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• 2011.04a
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• pp.1274-1277
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• 2011

단백질 1차 서열로부터 DISORDER와 ORDER지역을 예측하기 위해서 이 논문에서는 EP-tree에 기반한 출현패턴 발견 알고리즘을 제안하였다. EP-tree 알고리즘을 적용함으로서 기존의 단백질 특징 추출을 통한 방법과 달리 서열 자체에서 발견되는 출현패턴만을 이용하여 분류 모델을 생성하므로 기존의 신경망이나 SVM 보다 분류모델 생성 및 예측 속도가 빠르다. 또한 Disprot 4.9과 CASP7 테스트 데이터로 DISORDER/ORDER 지역을 예측한 결과, 73.4%의 높은 정확성을 보였다.

• Journal of Genetic Medicine
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• v.2 no.2
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• pp.53-57
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• 1998

Spinal muscular atrophy (SMA) type I is a common severe autosomal recessive inherited neuromuscular disorder that has been mapped to chromosome 5q11.2-13.3. The survival motor neuron (SMN) gene, a candidate gene, is known to be deleted in 96% of patients with SMA type I. Presently, PCR and single strand conformation polymorphism (PCR-SSCP) analyses have been made possible for application to both archival slides and paraffin-embedded tissues. Archival materials represent valuable DNA resources for genetic diagnosis. We applied these methods for the identification of SMN gene of SMA type I in archival specimens for the prenatal diagnosis. In this study, we performed the prenatal diagnosis with chorionic villus sampling (CVS) cells on two women who had experienced neonatal death of SMA type I. DNA extraction was done from archival slide and tissue materials and PEP-PCR was performed using CVS cells. In order to identify common deletion region of SMN and neuronal apoptosis-inhibitory protein (NAIP) genes, cold PCR-SSCP and PCR-restriction site assay were carried out. Case 1 had deletions of the exons 7 and 8, and case 2 had exon 7 only on the telomeric SMN gene. Both cases were found to be normal on NAIP gene. These results were the same for both CVS and archival biopsied specimens. In both cases, the fetuses were, therefore, predicted to be at very high risk of being affected and the pregnancy were terminated. These data clearly demonstrate that archival slide and paraffin-embedded tissues can be a valuable source of DNA when the prenatal genetic diagnosis is needed in case any source for genetic analysis is not readily available due to previous death of the fetus or neonate.