• 한국미생물·생명공학회지
• /
• 제25권6호
• /
• pp.560-565
• /
• 1997

DNA fragment assembly is a major concem in shot-gun DNA sequencing project. It is to reconstruct a consensus DNA sequence from a collection of random oritented fragments. We developed a computer program that is useful for DNA fragment assembly. Inputs to the program are DNA fragment sequences including IUB-IUPAC bases. The program produces the most probable reconstruction ot the original DNA sequence as a text format or a PostScript format. The program consists of four phases: the first phase quickly eliminates fragment pairs that can not possibly overlap. In the second phase, the quality of overlap between each pair is calculated to a score. In the third phase, overlap pairs are sorted by their scores and consistency of the overlaps is checked. The last phase determines consensus sequences and displays them. The performance of fragment assembly program was tested on a set of DNA fragment sequences which were generated from long DNA sequences of GenBank by a fragmentation program.

• Genomics & Informatics
• /
• 제7권1호
• /
• pp.46-48
• /
• 2009

Finishing is the most time-consuming step in sequencing, and many genome projects are left unfinished due to complex repeat regions. Here, we have developed BACContigEditor, a prototype shotgun sequence finishing tool. It is essentially an editor that visualizes assemblies of shotgun sequence fragment reads as gapped multiple alignments. The program offers some flexibility that is needed to rapidly resolve complex regions within a working session. The sole purpose of the release is to promote collaborative creation of extensible software for fragment assembly editors, foster collaborative development, and reduce barriers to initial tool development effort. We describe our software architecture and identify current challenges. The program is available under an Open Source license.

• 미생물학회지
• /
• 제34권1_2호
• /
• pp.58-63
• /
• 1998

'Contig 구성문제'는 random sequencing 단편들로부터 DNA 염기 서열의 정보를 밝혀낼 경우 발생하는 문제이다. 본 연구에서는 이러한 contig 구성문제를 해결하기 위한 알고리즘을 구성하였으며, X-window 응용 프로그램인 XFAP을 개발하였다. XFAP에서는 dimer 빈도 비교 방법을 사용하여 중첩 가능성이 없는 단편을 효과적으로 제거하였다. 이 방법은 단편 쌍 중첩에서 최소 수용 중첩 길이 내의 각 단편 사이의 dimer 빈도 차이를 이용하여 단편 쌍을 선별하는 것이다. 또한 단편 쌍 최대치 정렬 과정의 메모리 사용량을 줄이기 위해서, Myers 알고리즘을 적용하여 linear space에서 최대치 정렬을 구하는 방법을 사용하였다. 그리고 본 프로그램은 사용자들에게 편리한 그래픽 환경을 제공하기 위해서 Motif 라이브러리를 사용하여 X-window에서 구현되었다. 본 프로그램의 테스트 데이터를 생성하기 위해서 GenBank 데이터베이스에서 일정 길이의 염기 서열을 추출한 다음, sequencing시 일어날 수 있는 모든 오류들을 고려하여 단편 샘플을 생성하였다. 단편 샘플에 대해서 dimer 빈도 비교 방법의 효과 및 실행 시간을 측정하였다. 특히 dimer 빈도 비교 방법의 효율은 단편의 길이에 비례하여 증가하는 것으로 나타났다.

• Clinical and Experimental Reproductive Medicine
• /
• 제37권4호
• /
• pp.339-348
• /
• 2010

목적: 본 연구는 체외수정 및 배아이식술 (In vitro fertilization-embryo transfer, IVF-ET)에서 인간의 파편화된 배아를 대상으로 수행한 파편제거술이 배아의 발달과 임상적 결과에 미치는 유용한 결과를 조사하고자 수행하였다. 연구방법: 본 연구는 전향적 연구로서 한나여성의원과 미즈메디병원에서 수행되었으며 IVF-ET 시술을 받는 60명의 환자를 대상으로 하였다. 실험군으로서 29명 환자의 106개의 파편화된 배아를 대상으로 이식하기 전 미세수술적 파편 제거술을 수행하였고 대조군으로서 31명의 환자의 122개의 파편화된 배아의 파편을 제거하지 않고 이식하였다. 파편 제거술이 파편화된 배아의 형태학적 변화와 임상적 결과에 미치는 영향을 조사하였다. 결과: 실험군 배아의 평균 형태학적 등급은 G2.79였으나 파편제거술 이후 G1.63 (p<0.001)로 유의하게 향상되었다. 대부분의 파편화된 배아는 파편제거 후 이어지는 배양과정 동안 파편화 현상이 재 발생하지 않았으며 파편이 제거된 배아의 발달에 파편제거술이 유용한 효과를 미치는 것이 관찰되었다. 실험군의 착상률과 임신율은 각각 12.3%와 31.3%이었으나 대조군은 각각 6.6%와 22.5%를 나타내었다. 이러한 두 군간의 결과의 차이는 낮은 시술 건수로 인해 통계학적 유의성은 없었다. 결론: 미세수술적 파편제거술은 파편화된 배아의 형태학적 등급뿐만 아니라 지속적인 발달능력을 향상시켰다. 파편제거술은 파편에 의해 손상된 세포간 전달체계의 복원과 파편에 의한 해로운 물질의 생성 가능성을 제거함으로써 주위의 할구들에게 이로운 효과를 나타낸 것으로 생각된다.

• 한국CDE학회논문집
• /
• 제19권3호
• /
• pp.294-304
• /
• 2014

This paper presents a real-time rendering algorithm of large-scale geometric data using GLSL (OpenGL shading language). It details the VAO (vertex array object) and VBO(vertex buffer object) to be used for up-loading the large-scale point clouds and polygon meshes to a graphic video memory, and describes the shader program composed by a vertex shader and a fragment shader, which manipulates those large-scale data to be rendered by GPU. In addition, we explain the global rendering procedure that creates and runs the shader program with the VAO and VBO. Finally, a rendering performance will be measured with application examples, from which it will be demonstrated that the proposed algorithm enables a real-time rendering of large amount of geometric data, almost impossible to carry out by previous techniques.

• 한국환경성돌연변이발암원학회지
• /
• 제18권2호
• /
• pp.83-88
• /
• 1998

To detect the mutation in a given sequence, there are variety of methods developed by use of the gel electrophoresis. One of the methods, TGGE (Temperature Gradient Gel Electrophoresis), is a popular technique because it can detect mutations in DNA fragment with ease and at low cost. This study used 200 bp BamHI-digested DNA fragment containing the human $\varepsilon$-globin promoter which was mutated[$\varepsilon$ F1*(-141), GATA- I*(-163), and GATA-1* & $\varepsilon$F1]. This BamHI-digested DNA fragment was directly used to detect the mutated DNA fragment on 50% denaturant gel with temperature gradient of 45$^{\circ}C$ through $53^{\circ}C$. In agreement with the theoretical result of MELTSCAN program (Brossette and Wallet, 1994) the mobilities of mutated DNA fragments were shown to be nearly distinguished on the temperature gradient gel. In contrast to the above result the heteroduplex analysis under the temperature gradient condition was shown to detect the mutated DNA fragments through the heteroduplex formation between strands of mutated DNA and wild-type DNA.

• BMB Reports
• /
• 제29권1호
• /
• pp.52-57
• /
• 1996

A specific DNA fragment from Korean radish (Raphanus sativus L.) was amplified by performing PCR with oligonucleotide primers which correspond to the highly conserved regions of plant peroxidases. The size of the PCR product was ca. 400 bp, as expected from the known plant peroxidase genes. Comparison of the nucleotide and deduced amino acid sequences of the PCR product to those of other plant peroxidase-encoding genes revealed that the amplified fragment corresponded to the highly conserved region I and III of plant peroxidases. By screening a genomic library of Korean radish using the amplified fragment as a probe, two positive clones, named prxK1 and prxK2, were isolated. Restriction mapping studies indicated that the 5.2 kb Sail fragment of the prxK1 clone and the 4.0 kb EcoRI fragment of the prxK2 clone encode separate isoperoxidase genes. Analyses of the promoter region of the prxK1 clone shows that putative CAAT box, CMT box, and TGA1b binding sequence (5' TGACGT) are present 718 bp upstream from the start codon.

• Interdisciplinary Bio Central
• /
• 제2권2호
• /
• pp.6.1-6.5
• /
• 2010

Fragment molecular orbital (FMO) method provides a novel tool for ab initio calculations of large biomolecules. This method overcomes the size limitation difficulties in conventional molecular orbital methods and has several advantages compared to classical force field approaches. While there are many features in this method, we here focus on explaining the issues related to protein-ligand binding: FMO method provides useful interaction-analysis tools such as IFIE, CAFI and FILM. FMO calculations can provide not only binding energies, which are well correlated with experimental binding affinity, but also QSAR descriptors. In addition, FMO-derived charges improve the descriptions of electrostatic properties and the correlations between docking scores and experimental binding affinities. These calculations can be performed by the ABINIT-MPX program and the calculation results can be visualized by its proper BioStation Viewer. The acceleration of FMO calculations on various computer facilities is ongoing, and we are also developing methods to deal with cytochrome P450, which belongs to the family of drug metabolic enzymes.

• Journal of Microbiology and Biotechnology
• /
• 제16권1호
• /
• pp.118-125
• /
• 2006

The region responsible for replication of the megaplasmid pAtC58 in the nopaline-type Agrobacterium tumefaciens strain C58 was determined. A derivative ofa Co1E1 vector, pBluscript SK-, incapable of autonomous replication in Agrobacterium spp, was cloned with a 7.6-kb Bg1II-HindIII fragment from a cosmid clone of pAtC58, which contains a region adjacent to the operon for the utilization of deoxyfructosyl glutamine (DFG). The resulting plasmid conferred resistance to carbenicillin on the A. tumefaciens strain UIA5 that is a plasmidfree derivative of C58. The plasmid was stably maintained in the strain even after consecutive cultures for generations. Analysis of nested deletions of the 7.6-kb fragment showed that a 4.3-kb BglII-XhoI region sufficiently confers replication of the derivative of the ColE1 vector on UIA5. The region comprises three ORFs, which have high homologies with repA, repB, and repC of plasm ids in virulent Agrobacterium spp. including pTiC58, pTiB6S3, pTi-SAKURA, and pRiA4b as well as those of symbiotic plasmids from Rhizobium spp. Phylogenie analysis showed that rep genes in pAtC58 are more closely related to those in pRiA4 than to pTi plasmids including pTiC58, suggesting that the two inborn plasmids, pTiC58 and pAtC58, harbored in C58 evolved from distinct origins.

• Journal of Astronomy and Space Sciences
• /
• 제8권2호
• /
• pp.141-148
• /
• 1991

In order to obtain a complete picture of the time dependent dynamic of 360 fragments in space, the program IODS (ISSA Orbit Determination System) has been set up. Using The program IODS, all fragments orbits of one break-up event can be generated. Perturbations due to the Earth's asymmetrical potential, the Sun, moon, air drag and solar radiation force are considered. We summarize our results as follows : I) Due to J2 term, precessional motion of all fragment orbits are (수식생략) ii) The other perturbations have very small effects.