• Mycobiology
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• v.46 no.4
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• pp.361-369
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• 2018

The rice blast fungus, Magnaporthe oryzae, is an important pathogen of rice plants. It is well known that genes encoded in the genome have different evolutionary histories that are related to their functions. Phylostratigraphy is a method that correlates the evolutionary origin of genes with evolutionary transitions. Here we applied phylostratigraphy to partition total gene content of M. oryzae into distinct classes (phylostrata), which we designated PS1 to PS7, based on estimation of their emergence time. Genes in individual phylostrata did not show significant biases in their global distribution among seven chromosomes, but at the local level, clustering of genes belonging to the same phylostratum was observed. Our phylostrata-wide analysis of genes revealed that genes in the same phylostratum tend to be similar in many physical and functional characteristics such as gene length and structure, GC contents, codon adaptation index, and level of transcription, which correlates with biological functions in evolutionary context. We also found that a significant proportion of genes in the genome are orphans, for which no orthologs can be detected in the database. Among them, we narrowed down to seven orphan genes having transcriptional and translational evidences, and showed that one of them is implicated in asexual reproduction and virulence, suggesting ongoing evolution in this fungus through lineage-specific genes. Our results provide genomic basis for linking functions of pathogenicity factors and gene emergence time.

• International journal of advanced smart convergence
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• v.8 no.1
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• pp.1-8
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• 2019

Coronaviruses are known respiratory pathogens. In the past, most human coronaviruses were thought to cause mild symptoms such as cold. However recently, as seen in the Severe Acute Respiratory Syndrome (SARS) and the Middle East Respiratory Syndrome (MERS), infectious diseases with severe pulmonary disease and respiratory symptoms are caused by coronaviruses, making research on coronaviruses become important. Considering previous studies, we constructed 'HCoV-IMDB (Human Corona Virus Immune Database)' to systematically provide genetic information on human coronavirus and host immune information, which can be used to analyze the interaction between human coronavirus and host immune proteins. The 'HCoV-IMDB' constructed in the study can be used to search for genetic information on human coronavirus and host immune protein and to download data. A BLAST search specific to the human coronavirus, one of the database functions, can be used to infer genetic information and evolutionary relationship about the query sequence.

• Proceedings of the Korean Society for Information Management Conference
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• 2000.08a
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• pp.129-132
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• 2000

GIS(Geographic Information System) tool has been applied to determine a spatial difference of weed population density in paddy field and it has introduced to rice yield difference among counties as well as to rice blast in Korea. There was highly difference between sampling sites in terms of spatial analysis which may imply to be able to apply this tool for the precesion agriculture in the 21 century.

• BMB Reports
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• v.39 no.4
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• pp.441-447
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• 2006

Abuse of drugs can elicit compulsive drug seeking behaviors upon repeated administration, and ultimately leads to the phenomenon of addiction. We developed a procedure for the standardization of microarray gene expression data of rat brain in drug addiction and stored them in a single integrated database system, focusing on more effective data processing and interpretation. Another characteristic of the present database is that it has a systematic flexibility for statistical analysis and linking with other databases. Basically, we adopt an intelligent SQL querying system, as the foundation of our DB, in order to set up an interactive module which can automatically read the raw gene expression data in the standardized format. We maximize the usability of this DB, helping users study significant gene expression and identify biological function of the genes through integrated up-to-date gene information such as GO annotation and metabolic pathway. For collecting the latest information of selected gene from the database, we also set up the local BLAST search engine and non-redundant sequence database updated by NCBI server on a daily basis. We find that the present database is a useful query interface and data-mining tool, specifically for finding out the genes related to drug addiction. We apply this system to the identification and characterization of methamphetamine-induced genes' behavior in rat brain.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.8
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• pp.1144-1151
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• 2013

In this study, protein domains with cellulase activity in goat rumen microbes were investigated using metagenomic and bioinformatic analyses. After the complete genome of goat rumen microbes was obtained using a shotgun sequencing method, 217,892,109 pair reads were filtered, including only those with 70% identity, 100-bp matches, and thresholds below $E^{-10}$ using METAIDBA. These filtered contigs were assembled and annotated using blastN against the NCBI nucleotide database. As a result, a microbial community structure with 1431 species was analyzed, among which Prevotella ruminicola 23 bacteria and Butyrivibrio proteoclasticus B316 were the dominant groups. In parallel, 201 sequences related with cellulase activities (EC.3.2.1.4) were obtained through blast searches using the enzyme.dat file provided by the NCBI database. After translating the nucleotide sequence into a protein sequence using Interproscan, 28 protein domains with cellulase activity were identified using the HMMER package with threshold E values below $10^{-5}$. Cellulase activity protein domain profiling showed that the major protein domains such as lipase GDSL, cellulase, and Glyco hydro 10 were present in bacterial species with strong cellulase activities. Furthermore, correlation plots clearly displayed the strong positive correlation between some protein domain groups, which was indicative of microbial adaption in the goat rumen based on feeding habits. This is the first metagenomic analysis of cellulase activity protein domains using bioinformatics from the goat rumen.

• The Korean Journal of Mycology
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• v.40 no.3
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• pp.141-144
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• 2012

Total 50 species, 80 strains: Eighty strains of yeasts were isolated from wild flowers of Daejeon city and its surroundings in Korea. Isolated yeasts were identified by comparison of their PCR-amplified 18s rDNA V3 region or internal transcribed spacer-2 (ITS-2) genes with BLAST database. Among them, 32 species, 54 strains of yeasts were isolated and identified from wild flowers of Daejeon city, and Cryptococcus species were dominant yeasts. Furthermore, 18 species, 26 strains of yeasts were isolated and identified from wild flowers of Geumsan-gun and Nonsan-gun, Chungcheongnam-do in Korea, and also Candida species and Pseudozyma species were dominant yeasts.

• Journal of Life Science
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• v.11 no.1
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• pp.39-41
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• 2001

Cytohesin family has been thought to participate in inside-outside signaling linking growth factor receptor stimulation of PI 3-kinase to cell adhesion and stimulate nucleotide exchange of ARF through its Sec7 domain. The genomic structure of the cytohesin family was analyzed by BLAST search using cDNA and genomic DNA sequences from the GeneBank database. The cytohesin-2 was encoded by 12 exons. while the cytohesin-4 was encoded by 13 exons. The Sec7 and PH domains were not encoded by separate exons. In an analysis of retroviral integration, those two families did not contain any retroviral elements in introns or exons. The phylogenetic tree calculated by the neighbor-joining method suggests that the cytohesin-1 family was closely related to cytohesin-3 (ARNO3) family. These date could be of great use in further studies for resolving the exact function and evolution of the cytohesin family.

• Parasites, Hosts and Diseases
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• v.43 no.4 s.136
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• pp.149-156
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• 2005

Four hundred and sixty five randomly selected clones from a cDNA library of Blattella germanica were partially sequenced and searched using BLAST as a means of analyzing the transcribed sequences of its genome. A total of 363 expressed sequence tags (ESTs) were generated from 465 clones after editing and trimming the vector and ambiguous sequences. About $42\%$ (154/363) of these clones showed significant homology with other data base registered genes. These new B. germanica genes constituted a broad range of transcripts distributed among ribosomal proteins, energy metabolism, allergens, proteases, protease inhibitors, enzymes, translation, cell signaling path-ways, and proteins of unknown function. Eighty clones were not well-matched by database searches, and these rep-resent new B. germanica-specific ESTs. Some genes which drew our attention are discussed. The information obtained increases our understanding of the B. germanica genome.

• Explosives and Blasting
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• v.25 no.1
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• pp.67-77
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• 2007

The drill monitoring data are useful for the detection of abrupt and unexpected changes in ground renditions. This paper introduces a new approach to how drill performance parameters can be used for the prediction of quantitative rock mass properties ahead of tunnel face and the blasting design. The drill monitoring parameters available for the predictions include the instantaneous advance speed, thrust force, torque, tool pressure and penetration rate. The assessment of the drill monitoring parameters will be able to build a database provided that in-situ drill monitoring informations are accumulated and enable us to make a reasonable blast design based on quantitative assessment of rock mass.

• Journal of Mushroom
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• v.2 no.3
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• pp.145-148
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• 2004

This study was carried out to screen the fruiting body formation-specific genes from the medicinal mushroom Cordyceps militaris. A cDNA synthesized using total RNA from 4 stages of mushroom development, mycelium, primordium, immature fruiting body and mature fruiting body. Differential expression gene screening was performed by DD-PCR(Differential Display Arbitrary Primer PCR) with cDNA, we sequenced partial 6 genes using pGEM cloning vector. The DNA Sequence of the six DD-PCR products derived from differentially expressed genes was compared to that in the GenBank database by using the NCBI BLAST search to identify similarities to known sequences. Sequence analysis showed that six of DD-PCR products have unknown sequence.