• Title, Summary, Keyword: contig

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Draft genome sequences of Vibrio splendidus KCTC 11899BP, which produces hyaluronate lyase in the presence of hyaluronic acid (히알우론산 유도하에 히알우로네이트 라이아제를 생산하는 Vibrio splendidus KCTC 11899BP균주의 유전체 서열 분석)

  • Park, Joo Woong;Lee, Sang-Eun;Shin, Woon-Seob;Kim, Kyoung Jin;Kim, Youn Uck
    • Korean Journal of Microbiology
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    • v.54 no.3
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    • pp.302-304
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    • 2018
  • We, for the first time, isolated and identified a Vibrio splendidus KCTC 11899BP producing hyaluronate lyase from seawater. This enzyme is produced only when hyaluronic acid (HA) is added to the basal medium. Hyaluronate lyases are produced by microorganisms, which degrade the ${\beta}$-(1, 4) bond of HA to produce disaccharide. The genome of KCTC 11899BP, which consist of two circular contigs that are 3,522 kb (contig 1) long and 1,986 kb (contig 2) long respectively, as like other Vibrio sp. that contained 2 chromosomes. The genome included 4,700 predicted open reading frames, G + C content 44.12%, 137 tRNA genes, and 46 rRNA genes.

Development of an X-window Program, XFAP, for Assembling Contigs from DNA Fragment Data (DNA 염기 서열로부터 contig 구성을 위한 프로그램 XFAP의 개발)

  • Lee, Byung-Uk;Park, Kie-Jung;Kim, Seung-Moak
    • Korean Journal of Microbiology
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    • v.34 no.1_2
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    • pp.58-63
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    • 1998
  • Fragment assembly problem is to reconstruct DNA sequence contigs from a collection of fragment sequences. We have developed an efficient X-window program, XFAP, for assembling DNA fragments. In the XFAP, the dimer frequency comparison method is used to quickly eliminate pairs of fragments that can not overlap. This method takes advantage of the difference of dimer frequencies within the minimum acceptable overlap length in each fragment pair. Hirschberg algorithm is applied to compute the maximal-scoring overlapping alignment in linear space. The perfomance of XFAP was tested on a set of DNA fragment sequences extracted from long DNA sequences of GenBank by a fragmentation program and showed a great improvement in execution time, especially as the number of fragments increases.

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Development of Contig Assembly Program for Nucleotide Sequencing (염기서열 해독작업을 위한 핵산 단편 조립 프로그램의 개발)

  • 이동훈
    • Korean Journal of Microbiology
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    • v.35 no.2
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    • pp.121-127
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    • 1999
  • An effective computer program for assembling fragments in DNA sequencing has been developed. The program, called SeqEditor (Sequence Editor), is usable on the pcrsonal computer systems of MS-Widows which is the mosl popular operating system in Korea. It c'm recd several sequence file formats such as GenBak, FASTA, and ASCII. In the SeqEditor program, a dynamic programming algorihm is applied to compute the maximalscoring overlapping alignment between each pjlr of fragments. A novel feature of the program is that SeqEdilor implemnents interaclive operation with a graphical user interface. The performance lests of the prograln 011 fragmen1 data from 16s and 18s rDNA sequencing pi-ojects produced saiisIactory results. This program may be useful to a person who has work of time with large-scale DNA sequencing projects.

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A Base-Calling Error Detection Program for Use in Microbial Genome Projects (미생물 유전체 프로젝트 수행을 위한 Base-Calling 오류 감지 프로그램 및 알고리즘 개발)

  • Lee, Dae-Sang;Park, Kie-Jung
    • Korean Journal of Microbiology
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    • v.43 no.4
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    • pp.317-320
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    • 2007
  • In this paper, we have developed base-calling error detection program and algorithm which show the list of the genes or sequences that are suspected to contain base-calling errors. Those programs detect dubious bases in a few aspects in the process of microbial genome project. The first module detects base-calling error from the Phrap file by using contig assembly information. The second module analyzes frame shift mutation if it is originated from real mutation or artifact. Finally, in the case that there is control microbial genome annotation information, the third module extracts and shows the candidate base-calling error list by comparative genome analysis method.

Seed기반의 short read aligner 구현에 관한 연구

  • Ji, Mingeun;Kim, Jeongkyu;Yi, Gangman
    • Proceedings of the Korea Information Processing Society Conference
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    • pp.1107-1109
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    • 2019
  • 차세대 게놈 시퀀싱(NGS) 기술이 발전하면서 방대하게 축적된 유전체 데이터를 분석하기 위해 다양한 시퀀스 정렬 연구가 진행되고 있다. 시퀀스 정렬 중 잘 알려진 BLAST에서는 휴리스틱 기반의 시퀀스 정렬을 수행하여 긴 리드 시퀀스에 대해 속도와 안정성이 보장되지만 짧은 리드 시퀀스에 대해서는 성능이 저하되는 문제가 있다. 이 문제를 해결하기 위해 본 논문에서는 레퍼런스 시퀀스와 쿼리 시퀀스를 Seed 기반으로 분리하여 정렬을 수행한다. 최종적으로는 contig를 추출하고 레퍼런스-쿼리간 유효한 contig만 선별하여 빠르게 짧은 리드 시퀀스들의 정렬을 수행할 수 있는 정렬기를 구현하고자 한다.

A data management system for microbial genome projects

  • Ki-Bong Kim;Hyeweon Nam;Hwajung Seo and Kiejung Park
    • Proceedings of the Korean Society for Bioinformatics Conference
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    • pp.83-85
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    • 2000
  • A lot of microbial genome sequencing projects is being done in many genome centers around the world, since the first genome, Haemophilus influenzae, was sequenced in 1995. The deluge of microbial genome sequence data demands new and highly automatic data flow system in order for genome researchers to manage and analyze their own bulky sequence data from low-level to high-level. In such an aspect, we developed the automatic data management system for microbial genome projects, which consists mainly of local database, analysis programs, and user-friendly interface. We designed and implemented the local database for large-scale sequencing projects, which makes systematic and consistent data management and retrieval possible and is tightly coupled with analysis programs and web-based user interface, That is, parsing and storage of the results of analysis programs in local database is possible and user can retrieve the data in any level of data process by means of web-based graphical user interface. Contig assembly, homology search, and ORF prediction, which are essential in genome projects, make analysis programs in our system. All but Contig assembly program are open as public domain. These programs are connected with each other by means of a lot of utility programs. As a result, this system will maximize the efficiency in cost and time in genome research.

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Prediction of Core Promoter Region with Dependency - Reflecting Decomposition Model (의존성 반영 분해모델에 의한 유전자의 핵심 프로모터 영역 예측)

  • 김기봉;박기정;공은배
    • Journal of KIISE:Software and Applications
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    • v.30 no.3_4
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    • pp.379-387
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    • 2003
  • A lot of microbial genome projects have been completed to pour the enormous amount of genomic sequence data. In this context. the problem of identifying promoters in genomic DNA sequences by computational methods has attracted considerable research attention in recent years. In this paper, we propose a new model of prokaryotic core promoter region including the -10 region and transcription initiation site, that is Dependency-Reflecting Decomposition Model (DRDM), which captures the most significant biological dependencies between positions (allowing for non-adjacent as well as adjacent dependencies). DRDM showed a good result of performance test and it will be employed effectively in predicting promoters in long microbial genomic Contigs.

K-mer Based RNA-seq Read Distribution Method For Accelerating De Novo Transcriptome Assembly

  • Kwon, Hwijun;Jung, Inuk
    • Journal of the Korea Society of Computer and Information
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    • v.25 no.8
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    • pp.1-8
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    • 2020
  • In this paper, we propose a gene family based RNA-seq read distribution method in means to accelerate the overal transcriptome assembly computation time. To measure the performance of our transcriptome sequence data distribution method, we evaluated the performance by testing four types of data sets of the Arabidopsis thaliana genome (Whole Unclassified Reads, Family-Classified Reads, Model-Classified Reads, and Randomly Classified Reads). As a result of de novo transcript assembly in distributed nodes using model classification data, the generated gene contigs matched 95% compared to the contig generated by WUR, and the execution time was reduced by 4.2 times compared to a single node environment using the same resources.

Fragment Combination From DNA Sequence Data Using Fuzzy Reasoning Method (퍼지 추론기법을 이용한 DNA 염기 서열의 단편결합)

  • Kim, Kwang-Baek;Park, Hyun-Jung
    • Journal of the Korea Institute of Information and Communication Engineering
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    • v.10 no.12
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    • pp.2329-2334
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    • 2006
  • In this paper, we proposed a method complementing failure of combining DNA fragments, defect of conventional contig assembly programs. In the proposed method, very long DNA sequence data are made into a prototype of fragment of about 700 bases that can be analyzed by automatic sequence analyzer at one time, and then matching ratio is calculated by comparing a standard prototype with 3 fragmented clones of about 700 bases generated by the PCR method. In this process, the time for calculation of matching ratio is reduced by Compute Agreement algorithm. Two candidates of combined fragments of every prototype are extracted by the degree of overlapping of calculated fragment pairs, and then degree of combination is decided using a fuzzy reasoning method that utilizes the matching ratios of each extracted fragment, and A, C, G, T membership degrees of each DNA sequence, and previous frequencies of each A, C, G, T. In this paper. DNA sequence combination is completed by the iteration of the process to combine decided optimal test fragments until no fragment remains. For the experiments, fragments or about 700 bases were generated from each sequence of 10,000 bases and 100,000 bases extracted from 'PCC6803', complete protein genome. From the experiments by applying random notations on these fragments, we could see that the proposed method was faster than FAP program, and combination failure, defect of conventional contig assembly programs, did not occur.