• Title/Summary/Keyword: Tool Alignment

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MiRPI: Portable Software to Identify Conserved miRNAs, Targets and to Calculate Precursor Statistics

  • Vignesh, Dhandapani;Parameswari, Paul;Im, Su-Bin;Kim, Hae-Jin;Lim, Yong-Pyo
    • Genomics & Informatics
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    • v.9 no.1
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    • pp.39-43
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    • 2011
  • MicroRNAs (miRNAs) are recently discovered small RNA molecules usually resulting in translational repression and gene silencing. Despite the fact that specific cloning of small RNA's is a method in practice, computational identification of miRNA's has been a major focus recent days, since is a rapid process following AB initio and sequence alignment methods. Here we developed new software called MiRPI that aims to identify the highly conserved miRNAs without any mismatches from given fasta formatted gene sequences by using non-repeated miRNA dataset of the user's interest. The new window embedded with the software is used to identify the targets for inputted mature miRNAs in the mRNA sequences. Also MiRPI is designed to measure the precursor miRNA statistics, majorly focusing the Adjusted Minimum Folding free Energy (AMFE) and Minimum Folding free Energy Index (MFEI), the most important parameters in miRNA confirmation. MiRPI is developed by PERL (Practical Extraction and Report Language) and Tk (Tool kit widgets) scripting languages. It is user friendly, portable offline software that works in all windows OS, sized to 3 MB.

A Study on Determination Method of Radius and Transition Curve Length for Optimum Design in Curve (곡선부 선형 최적설계를 위한 적정 곡선반경-완화곡선장 결정기법 연구)

  • Um, Ju-Hwan;Kim, Eun-Kyum;Yang, Sin-Chu
    • Journal of the Korean Society for Railway
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    • v.12 no.2
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    • pp.199-204
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    • 2009
  • In this paper, a method for determining the boundary conditions which derived from the random obstacles on the curves was presented. A simple computer program using this method is also developed. This determination method and program can be used for a good engineering tool in optimal curve design and an Radius-transition curve length $(R-L_t)$ combination within the permissible zone can be improved without any increased costs.

Isolation and Identification of Yeasts from Wild Flowers Collected around Jangseong Lake in Jeollanam-do, Republic of Korea, and Characterization of the Unrecorded Yeast Bullera coprosmaensis

  • Han, Sang-Min;Hyun, Se-Hee;Lee, Hyang Burm;Lee, Hye Won;Kim, Ha-Kun;Lee, Jong-Soo
    • Mycobiology
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    • v.43 no.3
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    • pp.266-271
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    • 2015
  • Several types of yeasts were isolated from wild flowers around Jangseong Lake in Jeollanam-do, Republic of Korea and identified by comparing the nucleotide sequences of the PCR amplicons for the D1/D2 variable domain of the 26S ribosomal DNA using Basic Local Alignment Search Tool (BLAST) analysis. In total, 60 strains from 18 species were isolated, and Pseudozyma spp. (27 strains), which included Pseudozyma rugulosa (7 strains) and Pseudozyma aphidis (6 strains), was dominant species. Among the 60 strains, Bullera coprosmaensis JS00600 represented a newly recorded yeast strain in Korea, and its microbiological characteristics were investigated. The yeast cell has an oval-shaped morphology measuring $1.4{\times}1.7{\mu}m$ in size. Bullera coprosmaensis JS00600 is an asporous yeast that exhibits no pseudomycelium formation. It grew well in vitamin-free medium as well as in yeast extract-malt extract broth and yeast extract-peptone-dextrose (YPD) broth, and it is halotolerant growing in 10% NaCl-containing YPD broth.

groES Expression Related to Antifungal Activity of Streptomyces sp. SAR01 (Streptomyces sp. SAR01 균주에서의 항진균 관련 groES의 발현)

  • 이영근;김재성;조규성;장병일;추철형
    • Korean Journal of Microbiology
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    • v.38 no.3
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    • pp.162-167
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    • 2002
  • To analyse proteins and gene related to antifungal activity, SAR01 strain was isolated from a brown seaweed and identified as Streptomyces sp. by FAME(fatty acid methyl ester) analysis. Antifungal activity deficient mutant(SAR535) of Streptomyces sp. SAR01 was induced by gamma radiation$({60}^Co)$. It was found that 6 specific protein spots appeared only in SAR01 by 2-D electrophoresis analysis. Among them, a protein of 10 kDa had homology of 96% with 10 kD chaperonin cpn 10 (GroES) by Basic Local Alignment Search Tool(BLAST, NCBI) analysis. SAR535 transformants into which groES was transferred by electroporation revealed antifungal activity newly similar with SAR01 It suggested that groES be supposed to be related to the antifungal activity of Streptomyces sp. SAR01.

Determination of the Tooth Modification Amounts for Minimizing the Vibration of Helical Gear (헬리컬 치차의 진동최소화를 위한 치면 수정량의 결정)

  • Chong, Tae-Hyong;Myong, Jae-Hyong;Kim, Ki-Tae
    • Journal of the Korean Society for Precision Engineering
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    • v.17 no.11
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    • pp.199-205
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    • 2000
  • The vibration and noise of gears is due to the vibration exciting force caused by the tooth stiffness which changes periodically as the mesh of teeth proceeds and by the transmission error, that is, the rotation delay between driving gear and driven gear caused by manufacturing error and alignment error in assembly and so on. The purpose of this study is to develop how to calculate simultaneously the optimum amounts of tooth profile modification, end relief and crowning by minimizing the vibration exciting force of helical gears. We estimate the vibration exciting force by the mesh analysis of gears. The constraints of this problem consist of contact ratio and strengths of gear teeth such as tooth fillet stress, surface durability and scoring. ADS(Automated Design Synthesis) is used as an optimization tool. And, since the aspect ratio is an important parameter of tooth modification, we investigate the relation between it and the optimum values of tooth modification. The proposed method can calculate the optimum amount of tooth modification automatically and is to be utilized to resolve the problem of vibration of helical gears.

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Isolation of Three Unrecorded Yeasts from the Guts of Earthworms Collected from Korea

  • Oh, Hyejin;Kim, Myung Kyum
    • The Korean Journal of Mycology
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    • v.49 no.4
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    • pp.545-553
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    • 2021
  • In 2021, seven yeast strains were isolated from earthworm (Eisenia andrei) gut samples collected from the Nanji Water Regeneration Center in Goyang City, Gyeonggi Province, Korea. A total of seven yeasts were isolated, of which three strains have not been previously reported in Korea. To identify the yeasts, pairwise sequence comparisons of large subunit (LSU) rDNA sequences were performed using the basic local alignment search tool (BLAST). Assimilation test and cell morphology analysis were performed using the API 20C AUX kit and phase contrast microscope, respectively. Five of the seven strains were assigned to the genus Candida of the order Saccharomycetales of the class Saccharomycetes, and two to the genus Apiotrichum of the order Trichosporonales of the class Tremellomycetes. The yeast strain Candida sojae E2 belongs to the family Debaryomycetaceae, and Apiotrichum laibachii E8 and A. laibachii E9 belong to the family Trichosporonaceae. All strains were cultured in yeast mold agar for three days and showed different colony forms. C. sojae E2 was round and entire shaped, while A. laibachii E8 and A. laibachii E9 was round and convex shaped. This study focuses on the description of the three yeast strains that have not been officially reported in Korea.

Isolation of four unrecorded yeasts in the family Filobasidiaceae from soil in Korea

  • Maeng, Soohyun;Park, Yuna;Srinivasan, Sathiyaraj
    • Journal of Species Research
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    • v.10 no.4
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    • pp.350-355
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    • 2021
  • In 2020, 11 Basidiomycetous yeast strains were isolated from soil samples collected from the forests of Namhansanseong in Korea. Among them, seven species were reported, but four species were unreported in Korea. To identify wild yeasts, pairwise sequence comparisons of D1/D2 domain of the 26S rRNA were performed using Basic Local Alignment Search Tool (BLAST). The cell morphologies and assimilation test are observed by phase contrast microscope and API 20C AUX kit, respectively. The 11 strains were assigned to the genera Rhodotorula (4 strains) of the order Sporidiobolales of the class Microbotryomycetes; and Cryptococcus(2 strains), Goffeauzyma (1 strains), Naganishia (2 strains) of the order Filobasidiales and Saitozyma (2 strains) of the order Tremellales of the class Tremellomycetes in the phylum Basidiomycota. The unreported yeast strains Cryptococcus gastricus 20n5-2, Goffeauzyma gilvescens 20n2-7, Naganishia adeliensis 20n8-1, and Naganishia friedmannii 20n24-1 belong to the family Filobasidiaceae. All strains had oval shaped cells and cream-colored colonies cultured on on YM agar for 3 days. In this study, we focus on the description of four unreported yeast species in Korea.

A Genome-Wide Analysis of Antibiotic Producing Genes in Streptomyces globisporus SP6C4

  • Kim, Da-Ran;Kwak, Youn-Sig
    • The Plant Pathology Journal
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    • v.37 no.4
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    • pp.389-395
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    • 2021
  • Soil is the major source of plant-associated microbes. Several fungal and bacterial species live within plant tissues. Actinomycetes are well known for producing a variety of antibiotics, and they contribute to improving plant health. In our previous report, Streptomyces globisporus SP6C4 colonized plant tissues and was able to move to other tissues from the initially colonized ones. This strain has excellent antifungal and antibacterial activities and provides a suppressive effect upon various plant diseases. Here, we report the genome-wide analysis of antibiotic producing genes in S. globisporus SP6C4. A total of 15 secondary metabolite biosynthetic gene clusters were predicted using antiSMASH. We used the CRISPR/Cas9 mutagenesis system, and each biosynthetic gene was predicted via protein basic local alignment search tool (BLAST) and rapid annotation using subsystems technology (RAST) server. Three gene clusters were shown to exhibit antifungal or antibacterial activity, viz. cluster 16 (lasso peptide), cluster 17 (thiopeptide-lantipeptide), and cluster 20 (lantipeptide). The results of the current study showed that SP6C4 has a variety of antimicrobial activities, and this strain is beneficial in agriculture.

Isolation and characterization of four unrecorded wild yeasts from the soils of Republic of Korea in winter

  • Yuna Park;Soohyun Maeng;Sathiyaraj Srinivasan
    • Journal of Species Research
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    • v.12 no.3
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    • pp.197-202
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    • 2023
  • The purpose of this study was to isolate and identify wild yeasts from the soil collected in Gwangju and Pocheon City, Gyeonggi Province, Republic of Korea. Among 10 strains, six strains were already reported, but four strains were unrecorded in Republic of Korea. To identify wild yeast strains, pairwise sequence comparisons of the D1/D2 region of the 26S rRNA gene sequence were performed using Basic Local Alignment Search Tool (BLAST). The cell morphologies were observed by phase contrast microscope and assimilation tests were carried out using API 20C AUX kit. The 10 strains were assigned to the phyla Basidiomycota (8 strains) and Ascomycota (2strains). The unrecorded four yeast strains, NH33, NH19, NH20, and YP416, belong to the phylum Basidiomycota and the genera Buckleyzyma, Leucosporidium, Holtermanniales, and Mrakia, respectively. All strains had oval-shaped and polar budding cells. In this research, the morphological and biochemical properties of four unreported yeast species were characterized intensively, which were not officially reported in Korea.

Development of a tool to generate diploid genome sequences for whole-genome alignments. (이배체 유전체들의 서열비교를 위한 유전체 염기서열 생성도구 개발)

  • Kim, Jonghyun;Park, Chihyun;Park, Sanghyun
    • Proceedings of the Korea Information Processing Society Conference
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    • 2007.11a
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    • pp.272-273
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    • 2007
  • 현대 유전체학 기술의 진보는 생물학적으로 중요한 의미를 갖는 생물들의 유전체 서열의 규명 genome sequencing)에 힘입은 바 크다. 기존의 유전체 서열결정법은 주로 염기변이율이 낮은 생물들에 초점을 맞추어 왔다. 하지만 염기변이율이 높은 생물들의 유전체 염기서열을 결정할 필요가 높아짐에 따라 이를 위한 방법론에 대한 연구가 활발히 진행되고 있다. 염기변이율이 높은 생물들의 이배체 (diploid) 유전체 서열이 효과적으로 결정될 수 있을 경우 기존의 유전체 서열비교의 방법론에도 변화가 요청되고 있는 실정이다. 기존의 유전체 서열비교 (whole-genome alignment) 방법론은 반수체 (haploid) 유전체들의 서열비교을 위해 개발되었지만, 염기변이율이 높은 생물들의 유전체 서열비교에는 반수체 유전체들 비교에 특화된 도구들이 필요하다. 또한 현재 서열비교를 시각화하는 소프트웨어들도 반수체 유전체 비교를 위해 개발된 실정이다. 본 논문의 목표는 이배체 유전체 서열을 비교하는 방법론을 개발을 용이하기위해 이배체 유전체의 서열을 생성하는 도구를 개발하는 것이다. 개발된 도구는 실제 일어날 수 있는 염기변이와 genomic rearrangement를 사용자의 입력을 받아 다수의 생물들의 유전체 서열을 생성해 낸다. 이를 통해 이배체 유전체 서열을 비교하는 도구의 개발을 용이하게 하는데 초첨을 맞추고 있다.