• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2003.10a
• /
• pp.200-209
• /
• 2003

주어진 염기서열에서 유전자 영역을 예측하는 유전자 구조 예측은 유전체 프로젝트의 중요한 과정 중 하나이며 유전체 프로젝트 전체에 큰 영향을 준다. 진핵생물의 유전체가 원핵생물의 유전체에 비해 더 복잡한 구조를 가지기 때문에 진핵생물의 유전자 구조 예측 모델 역시원핵생물에 비해 다양한 모델이 제안되었다. 본 연구팀은 duration hidden markov model을 기본형태로 하여 EGSP(Eukaryotic Gene Structure Prediction)프로그램을 개발하였다. 현재 개발된 진핵생물의 유전자 구조 예측 알고리즘 중에서 GenScan이 가장 정교한 젓으로 보고 되고 있는데, EGSP의 결과분석을 위해 Genscan과 함께 GeneID, Morgan의 예측결과를 여러 가지 기준에서 비교하였다. EGSP는 정교한 예측모델을 가지고 있음에도 각 구성모듈에 대한 파라메터의 정교함에서 부족한 면이 나타나므로, 모델의 개선과 각 모듈의 조율을 통해 더욱 개선된 결과를 가지게 될 것이다.

• Journal of Life Science
• /
• v.24 no.7
• /
• pp.791-797
• /
• 2014

Sixty-two conserved orthologous groups (OGs) of proteins, in 63 prokaryotes and seven eukaryotes were analyzed to identify essential proteins in the mitochondria of eukaryotes, and their counterparts in prokaryotes. Twenty OGs were common in eukaryotic mitochondria, and all were translation related. Encephalitozoon cuniculi, an obligate parasitic eukaryote, shares no common mitochondrial OGs with the other 69 organisms. Seventeen conserved OGs were mitochondria related in the 69 organisms. Mitochondria related- and nonrelated-OGs were divided into prokaryotic genomes (p<0.001, paired t-test) unlike eukaryotic genomes in the distance value analysis. The most commonly conserved mitochondria-related OG was COG0048-KOG1750 (ribosomal small subunit S12), whereas it was COG0100-KOG0407 (ribosomal small subunit S11) in nonrelated OGs. These results could be applied in scientific research to determine phylogenetic relationships and in areas such as drug development.

• Korean Journal of Microbiology
• /
• v.39 no.4
• /
• pp.207-215
• /
• 2003

Gene structure prediction, which is to predict protein coding regions in a given nucleotide sequence, is the most important process in annotating genes and greatly affects gene analysis and genome annotation. As eukaryotic genes have more complicated stuructures in DNA sequences than those of prokaryotic genes, analysis programs for eukaryotic gene structure prediction have more diverse and more complicated computational models. We have developed EGSP, a eukaryotic gene structure program, using duration hidden markov model. The program consists of two major processes, one of which is a training process to produce parameter values from training data sets and the other of which is to predict protein coding regions based on the parameter values. The program predicts multiple genes rather than a single gene from a DNA sequence. A few computational models were implemented to detect signal pattern and their scanning efficiency was tested. Prediction performance was calculated and was compared with those of a few commonly used programs, GenScan, GeneID and Morgan based on a few criteria. The results show that the program can be practically used as a stand-alone program and a module in a system. For gene prediction of eukaryotic microbial genomes, training and prediction analysis was done with Saccharomyces chromosomes and the result shows the program is currently practically applicable to real eukaryotic microbial genomes.

• Proceedings of the Korea Contents Association Conference
• /
• 2016.05a
• /
• pp.193-194
• /
• 2016

세포사멸(apoptosis)이란 유전자에 의해 제어되는 세포의 능동적인 죽음을 의미하며 진핵세포만이 가지는 기작으로 세포자살을 일컫는 말이다. 단백질 정보 DB인 UNIPROT으로부터 진핵 생물 종의 세포사멸 단백질(apoptotic protein)을 수집하여 아미노산 서열에 대한 서열비교분석(alignment)을 진행하였다. 그 결과에 따라 다양한 종에 걸쳐 그 서열이 유사하게 유지되는 세포사멸 단백질을 중심단백질로 선정하였다. 비교단백체 분석을 통해서 생물 계통도에서 보여지는 생명종과 이들 단백질과의 연계성을 비교 분석함으로써 단순한 진핵세포에서 점진적으로 확대되는 종까지의 세포사멸 과정을 추론하였다.

• Journal of the Institute of Convergence Signal Processing
• /
• v.6 no.1
• /
• pp.27-32
• /
• 2005

As a large quantity of Genome sequencing has happened to be done a very much a surprising speed in short period, an automatic genome annotation process has become prerequisite. The most difficult process among with this kind of genome annotation works is to finding out the protein-coding genes within a genome. The main 2 subjects of gene prediction are Eukaryotes and Prokaryotes ; their genes have different structures, therefore, their gene prediction methods will also obviously varies. Until now, it is found that among of the 231 genome sequenced species, 200 have been found to be prokaryotes, therefore, for study of biotechnology studies, through comparative genomics, prokaryotes, rather than eukaryotes could may be more appropriate than eukaryotes. Even more, prokaryotes does not have the gene structure called an intron, so it makes the gene prediction easier. Former prokaryotes gene predictions have been shown to be 80%～ to 90% of accuracy. A recent study is aiming at 100% of gene prediction accuracy. In this paper, especially in the case of the E. coli K-12 and S. typhi genomes, gene prediction accuracy which showed 98.5% and 98.7% was more efficient than previous GLIMMER.

• Journal of Life Science
• /
• v.23 no.4
• /
• pp.595-601
• /
• 2013

The clusters of orthologous groups of proteins (COG) algorithm was applied to identify essential proteins in eukaryotes and to measure the degree of conservation. Sixty-three orthologous groups, which were conserved in 66 microbial genomes, enlarged to 104 eukaryotic orthologous groups (KOGs) and 71 KOGs were conserved at the nuclear genome of 7 eucaryotes. Fifty-four of 71 translation-related genes were conserved, highlighting the importance of proteins in modern organisms. Translation initiation factors (KOG0343, KOG3271) and prolyl-tRNA synthetase (KOG4163) showed high conservation based on the distance value analysis. The genes of Caenorhabditis elegans appear to harbor high genetic variation because the genome showed the highest variation at 71 conserved proteins among 7 genomes. The 71 conserved genes will be valuable in basic and applied research, for example, targeting for antibiotic development.

• Korean Journal of Microbiology
• /
• v.24 no.4
• /
• pp.400-405
• /
• 1986

We have constructed a phylogenetic tree for eleven species by comparing their tRNA sequences. The tree suggests that prokaryotes diverged very early before the emergence of animals. The fact that H. volcano, an archaebacterium, clusters with eukaryotes implied that eukaryotes did not diverge directly from thier common ancestor with eubacteria. The branching order of phage $T_{4}$ and phage $T_{5}$ indicates that they have diverged separately from thier hosts and they might have evolved independently. A correlation between nucleotide substitution in tRNAs and paleontological record was observed. We verified that our phylogenetic tree fits very well with traditional ones very well by imposing the molecular clock on the tree.

• The Journal of the Institute of Internet, Broadcasting and Communication
• /
• v.11 no.4
• /
• pp.113-118
• /
• 2011

Sequence homology analysis in the substances in the phenomenon of life is to create database by sorting and indexing and to demonstrate the usefulness of informatics. In this paper, Markov models are used in GenScan program to convert the pattern of complex eukaryotic protein sequences. It becomes impossible to navigate the minimum distance, complexity increases exponentially as the exact calculation. It is used scorecard in amino acid substitutions between similar amino acid substitutions to have a differential effect score, and is applied the Markov models sophisticated concealment of the transition probability model. As providing superior method to translate sequences homologous sequences in analysis using blast p, Markov models. is secreted protein structure of sequence translations.

• Korean Journal of Microbiology
• /
• v.46 no.1
• /
• pp.96-103
• /
• 2010

Oligosaccharyltransferase (OTase) catalyzes the transfer of a lipid-linked oligosaccharide (LLO) to the nascent polypeptide. Most eukaryotes have an OTase composed of a multisubunit protein complex. However, the kinetoplastid Leishmania major and the bacterium Campylobacter jejuni have only a single subunit for OTase activity, Stt3p and PglB, respectively. In this study, a new in vitro assay for OTase was developed by using a fluorescent peptide containing N-glycosylation sequon, Asn-Xaa-Thr/Ser, where Xaa can be any amino acid residue except Pro. L. major Stt3p and C. jejuni PglB as a model OTase enzyme demonstrated the formation of glycopeptides from a fluorescent peptide through OTase activities. For separation and measurement of the glycopeptides produced by the OTases, Tricine-SDS-PAGE, a lectin column and fluorospectrophotometer, and HPLC were applied. Comparison of these assay methods for analyzing a fluorescent glycopeptide showed HPLC analysis is the best method for separation of glycopeptides and nonglycosylated peptides as well as for quantify the peptides than other methods.

• Korean Journal of Microbiology
• /
• v.28 no.2
• /
• pp.128-133
• /
• 1990

The chromatin of all higher eukaryotic cells contains a group of very basic low-mole-cular weight proteins, the histones. But much less is known about histones in lower eukaryotes. Our purpose was to study the histones of the genus Rhizopus. After isolation and purification of nucleoprotein the basic nucleoproteins were analyzed by gel electrophoresis, in sodium dodecyl sulfate as well as acid/urea gels and compared with calf thymus histones. Their electrophoretic mobility in polyacrylamide gel indicate that they are histone homologous, although not identical, to the H2A, H2B, H3 and H4 histones of mammals with the exception of H1. The result suggests that Rhizopus thus appears to contain histone proteins which are homologous to the histones from in higher eukaryotes. The similarity between the calf thymus histone H1 and the Rhizopus high band group remains to be discussed.