• Korean Journal of Microbiology
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• v.35 no.2
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• pp.115-120
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• 1999

Multiple Sequence Alignment of DNA and protem sequences is a imnport'mt tool in the study of molecular evolution, gene regulation. and prolein suucture-function relationships. Progressive pairwise alignment method generates multiple sequence alignment fast but not necessarily with optimal costs. Dynamic programming generates multiple sequence alig~~menl with optimal costs in most cases but long execution time. In this paper. we suggest genetlc algorithm lo improve the multiple sequence alignment generated from the cnlent methods, describe the design of the genetic algorithm, and compare the multiple sequence alignments from 0111 method and current methods.

• Genomics & Informatics
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• v.16 no.4
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• pp.23.1-23.5
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• 2018

Virus taxonomy was initially determined by clinical experiments based on phenotype. However, with the development of sequence analysis methods, genotype-based classification was also applied. With the development of genome sequence analysis technology, there is an increasing demand for virus taxonomy to be extended from in vivo and in vitro to in silico. In this study, we verified the consistency of the current International Committee on Taxonomy of Viruses taxonomy using an in silico approach, aiming to identify the specific sequence for each virus. We applied this approach to norovirus in Caliciviridae, which causes 90% of gastroenteritis cases worldwide. First, based on the dogma "protein structure determines its function," we hypothesized that the specific sequence can be identified by the specific structure. Firstly, we extracted the coding region (CDS). Secondly, the CDS protein sequences of each genus were annotated by the conserved domain database (CDD) search. Finally, the conserved domains of each genus in Caliciviridae are classified by RPS-BLAST with CDD. The analysis result is that Caliciviridae has sequences including RNA helicase in common. In case of Norovirus, Calicivirus coat protein C terminal and viral polyprotein N-terminal appears as a specific domain in Caliciviridae. It does not include in the other genera in Caliciviridae. If this method is utilized to detect specific conserved domains, it can be used as classification keywords based on protein functional structure. After determining the specific protein domains, the specific protein domain sequences would be converted to gene sequences. This sequences would be re-used one of viral bio-marks.

• Journal of Life Science
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• v.27 no.1
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• pp.89-94
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• 2017

DNA sequences of the intergenic spacer 1 and intergenic spacer 2 of the nineteen plants belonging Vitis genus were collected from the Genbank. DNA sequences of the same regions of Vitis thunbergii var. sinuata and Ampelopsis brevipedunculata var. heterophylla, both common plants in Korea, were not available in Genbank. Those two plants were collected, their genomic DNA encoding 18S rRNA, intergenic spacer 1, 5.8S rRNA, intergenic spacer 2 and part of 28S rRNA amplified and DNA sequence determined. DNA sequences of twenty-one plants including two Korean plants were aligned by the Multiple sequence comparison by log-expectation(MUSCLE) algorithm and the alignment was used to calculate neighbor-joining tree and pairwise distance. The results indicate DNA sequences of the two Korean plants are highly homologous with each other, but they are quite distantly related to the other Vitis plants. Distant relationship of the two Korean plants with the other Vitis plants might be due to independent evolution of those two plants in geographically isolated environment. Those two Korean plants are classified in different genera based on the morphology, one in Vitis genus and the other in Ampelopsis genus, providing another example of discrepancy between morphological and genetic classification.

• The Journal of the Korea Contents Association
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• v.14 no.4
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• pp.407-417
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• 2014

An arirang is the most famous Korean folk song and was registered in UNESCO(Unitied Nations Educational, Scientific and cultural Organization) as an intangible cultural heritage in 2012. Most arirangs are composed of text and refrain parts. Genealogy of the arirang was classified in refrain patterns by using multiple sequence alignment algorithm. There are two different refrain patterns, slow and fast melodies. Of 106 arirangs, 38 and 68 arirangs contain fast and slow melodies, respectively. 73 arirangs and 104 their key words were extracted from bipartate arirang network that composed of arirangs, text works, and their relationships. The correlation among the arirangs was analyzed from the selected arirangs and key words by using pairwise comparison matrix. Also, analysis of correlation among the arirnags was performed by stepwise removal of the single degree nodes from the bipartate arirang network In this study, arirangs were analyzed in genealogy and correlation among arirangs by using informatic algorithm and network technology, in which arirang research will be constructed a stepping stone for the popularization and globalization of the arirangs.