• Genomics & Informatics
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• v.2 no.2
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• pp.86-91
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• 2004

Even though it represents $6-13\%$ of human genomic DNA, Alu sequences are rarely found in coding regions. When in exon region, over $80\%$ of them are found in 3' untranslated region (UTR). Pseudogenes are an important component of human genome. Their functions are not clearly known and the mechanism of how they are generated is still debatable. Both the Alu and Pseudogenes are important research problems in molecular biology. mRNA is thought to be a prime source of pseudogene and active research is going on its molecular mechanism. We report, for the first time, that mRNAs containing Alu repeats at 3' UTR has a significantly high correlation with processed pseudogenes, suggesting a possibility that Alu containing mRNAs have a high tendency to become processed pseudogenes. It is known that about $10\%$ of all human genes have been transposed. Transposed genes at 3' UTR without Alu repeat have about two processed pseudogenes per gene on average while we found with statistical significance that a transposed gene with Alu had over three processed Pseudogenes on average. Therefore, we propose Alu repeats as a new and important factor in the generation of pseudogenes.

• Archives of Pharmacal Research
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• v.22 no.6
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• pp.542-548
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• 1999

The UL47 gene (b 60390-b 60388) located in the unique long region of the human cytomegalovirus (HCMV) AD169 strain genome was analyzed RNA mapping. Northern blot analysis showed that the UL47 gene was expressed at late times after infection (72 h postinfection). The 9.7-kb transcript was expressed in the infected cells but not in phosphonoformate-treated cells at 72 hpi, indicating that the UL47 gene was only expressed at late times after infection. To map the 5'-end and 3'-end of UL47 transcripts, primer at late times after infection. To map the 5'-end and 3'-end of UL47 transcripts, primer extension and RNase protection analysis were performed. Primer extension analysis revealed that the transcription initiation site of UL47 was located in 27 bp downstream (b 60323) of the TATA box motif. The sizes of UL47 ORF (approximately 2.9-kb) and UL48 ORF (approximately 6.7-kb) deduced from computer sequence analysis suggest that the expressed 9.7-kb transcript of UL47 uses the 3'-end polyadenylation signal of Ul48. The result of RNase protection determined that the 3'-end of UL47 RNA utilized the 3'-end polyadenylation signal of UL48, which is located in HCMV genome b 70082.

• Genomics & Informatics
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• v.11 no.4
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• pp.289-291
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• 2013

Human papillomavirus (HPV) infection is the leading cause of cancer mortality among women worldwide. The molecular understanding of HPV proteins has significant connotation for understanding their intrusion in the host and designing novel protein vaccines and anti-viral agents, etc. Genomic, proteomic, structural, and disease-related information on HPV is available on the web; yet, with trivial annotations and more so, it is not well customized for data analysis, host-pathogen interaction, strain-disease association, drug designing, and sequence analysis, etc. We attempted to design an online reserve with comprehensive information on HPV for the end users desiring the same. The Human Papillomavirus Proteome Database (hpvPDB) domiciles proteomic and genomic information on 150 HPV strains sequenced to date. Simultaneous easy expandability and retrieval of the strain-specific data, with a provision for sequence analysis and exploration potential of predicted structures, and easy access for curation and annotation through a range of search options at one platform are a few of its important features. Affluent information in this reserve could be of help for researchers involved in structural virology, cancer research, drug discovery, and vaccine design.

• Korean Journal of Microbiology
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• v.53 no.2
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• pp.129-130
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• 2017

Streptococcus gordonii is a Gram-positive, facultative anaerobic and non-motile cocci. S. gordonii is a member of oral flora and a pioneer species that initiate the dental biofilm formation. S. gordonii has also been implicated in the pulpitis of primary teeth as well as systemic diseases such as infective endocarditis and septic arthritis. S. gordonii is associated with oral, respiratory, and gastrointestinal tract infections. S. gordonii KCOM 1506 (= ChDC B679) was isolated from a human acute pulpitis lesion. Here, we present the complete genome sequence of S. gordonii KCOM 1506.

• Korean Journal of Microbiology
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• v.53 no.2
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• pp.131-133
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• 2017

Streptococcus intermedius is a Gram-positive, obligately anaerobic, nonsporeforming, and nonmotile cocci. S. intermedius is a member of oral flora and is endodontic infection, respiratory infections, infective endocarditis, brain abscess, and liver abscess. Streptococcus intermedius ChDC B718 (= KCOM 1545) was isolated from a human pulpitis lesion. Here, we present the complete genome sequence of S. intermedius ChDC B718.

• Korean Journal of Microbiology
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• v.53 no.2
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• pp.123-125
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• 2017

Parvimonas micra is a Gram-positive, obligately anaerobic, non-spore forming, and non-motile cocci. P. micra is a member of oral flora and is associated with oral, respiratory, and gastrointestinal tract infections. Parvimonas micra KCOM 1535 (=ChDC B708) was isolated from a human periapical abscess lesion. Here, we present the complete genome sequence of P. micra KCOM 1535.

• Korean Journal of Microbiology
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• v.53 no.4
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• pp.334-336
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• 2017

Porphyromonas gingivalis is a Gram-negative, obligately anaerobic, and nonmotile rod. P. gingivalis is a pathogen of periodontitis and endodontic infection as well as is associated with systemic diseases including atherosclerosis, preterm, and Alzheimer's diseases. P. gingivalis KCOM 2797 (= JS2) was isolated from a human periodontitis lesion. Here, we present the draft genome sequence of P. gingivalis KCOM 2797.

• Korean Journal of Microbiology
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• v.55 no.1
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• pp.52-54
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• 2019

Dialister pneumosintes is a Gram-staining-negative, anaerobic, non-fermenting, and rod-shaped bacterium. D. pneumosintes is considered to be a periodontal pathogen. D. pneumosintes KCOM 1685 (= ChDC B414) was isolated from a human postoperative maxillary cyst lesion. In this report, we present the draft genome sequence of D. pneumosintes KCOM 1685.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• v.16 no.2
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• pp.71-79
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• 2013

The human-associated microbiota is diverse, varies between individuals and body sites, and is important in human health. Microbes in human body play an essential role in immunity, health, and disease. The human microbiome has been studies using the advances of next-generation sequencing and its metagenomic applications. This has allowed investigation of the microbial composition in the human body, and identification of the functional genes expressed by this microbial community. The gut microbes have been found to be the most diverse and constitute the densest cell number in the human microbiota; thus, it has been studied more than other sites. Early results have indicated that the imbalances in gut microbiota are related to numerous disorders, such as inflammatory bowel disease, colorectal cancer, diabetes, and atopy. Clinical therapy involving modulating of the microbiota, such as fecal transplantation, has been applied, and its effects investigated in some diseases. Human microbiome studies form part of human genome projects, and understanding gleaned from studies increase the possibility of various applications including personalized medicine.

• Genomics & Informatics
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• v.18 no.1
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• pp.5.1-5.5
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• 2020

Highly pathogenic avian influenza (HPAI) viruses have caused severe respiratory disease and death in poultry and human beings. Although most of the avian influenza viruses (AIVs) are of low pathogenicity and cause mild infections in birds, some subtypes including hemagglutinin H5 and H7 subtype cause HPAI. Therefore, sensitive and accurate subtyping of AIV is important to prepare and prevent for the spread of HPAI. Next-generation sequencing (NGS) can analyze the full-length sequence information of entire AIV genome at once, so this technology is becoming a more common in detecting AIVs and predicting subtypes. However, an analysis pipeline of NGS-based AIV sequencing data, including AIV subtyping, has not yet been established. Here, in order to support the pre-processing of NGS data and its interpretation, we developed a user-friendly tool, named prediction of avian influenza virus subtype (PAIVS). PAIVS has multiple functions that support the pre-processing of NGS data, reference-guided AIV subtyping, de novo assembly, variant calling and identifying the closest full-length sequences by BLAST, and provide the graphical summary to the end users.