• Genomics & Informatics
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• v.16 no.4
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• pp.29.1-29.5
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• 2018

Hybrid capture-based targeted sequencing is being used increasingly for genomic variant profiling in tumor patients. Unique molecular index (UMI) technology has recently been developed and helps to increase the accuracy of variant calling by minimizing polymerase chain reaction biases and sequencing errors. However, UMI-adopted targeted sequencing data analysis is slightly different from the methods for other types of omics data, and its pipeline for variant calling is still being optimized in various study groups for their own purposes. Due to this provincial usage of tools, our group built an analysis pipeline for global application to many studies of targeted sequencing generated with different methods. First, we generated hybrid capture-based data using genomic DNA extracted from tumor tissues of colorectal cancer patients. Sequencing libraries were prepared and pooled together, and an 8-plexed capture library was processed to the enrichment step before 150-bp paired-end sequencing with Illumina HiSeq series. For the analysis, we evaluated several published tools. We focused mainly on the compatibility of the input and output of each tool. Finally, our laboratory built an analysis pipeline specialized for UMI-adopted data. Through this pipeline, we were able to estimate even on-target rates and filtered consensus reads for more accurate variant calling. These results suggest the potential of our analysis pipeline in the precise examination of the quality and efficiency of conducted experiments.

• Journal of Microbiology and Biotechnology
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• v.26 no.1
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• pp.207-212
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• 2016

PacBio's long-read sequencing technologies can be successfully used for a complete bacterial genome assembly using recently developed non-hybrid assemblers in the absence of second-generation, high-quality short reads. However, standardized procedures that take into account multiple pre-existing second-generation sequencing platforms are scarce. In addition to Illumina HiSeq and Ion Torrent PGM-based genome sequencing results derived from previous studies, we generated further sequencing data, including from the PacBio RS II platform, and applied various bioinformatics tools to obtain complete genome assemblies for five bacterial strains. Our approach revealed that the hierarchical genome assembly process (HGAP) non-hybrid assembler resulted in nearly complete assemblies at a moderate coverage of ~75x, but that different versions produced non-compatible results requiring post processing. The other two platforms further improved the PacBio assembly through scaffolding and a final error correction.

• Genomics & Informatics
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• v.6 no.2
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• pp.87-90
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• 2008

During the last four years, the pyrosequencing-based 454 platform has rapidly displaced the traditional Sanger sequencing method due to its high throughput and cost effectiveness. Meanwhile, the Sanger sequencing methodology still provides the longest reads, and paired-end sequencing that is based on that chemistry offers an opportunity to ensure accurate assembly results. In this report, we describe an optimized approach for hybrid de novo genome assembly using pyrosequencing data and varying amounts of Sanger-type reads. 454 platform-derived contigs can be used as single non-breakable virtual reads or converted to simpler contigs that consist of editable, overlapping pseudoreads. These modified contigs maintain their integrity at the first jumpstarting assembly stage and are edited by fragmenting and rejoining. Pre-existing assembly software then can be applied for mixed assembly with 454-derived data and Sanger reads. An effective method for identifying genomic differences between reference and sample sequences in whole-genome resequencing procedures also is suggested.

• 한국정보통신설비학회:학술대회논문집
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• 2008.08a
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• pp.486-490
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• 2008

본 논문에서는 Spurious NAK Suppression알고리즘을 통하여 RLP의 성능향상에 대한 기법을 제안한다. 일반적으로, Hybrid ARQ기법에서는 MAC과 Physical Layer에서의 Retransmission 및 Error Correction으로 무선환경에서의 Error를 줄이고 latency를 보장하고 있다. 그러나 Hybrid ARQ에서의 Multiple SAW나 Selective-ARQ에 의해서 인접한 Packet들 간의 out-of-sequence문제가 발생할 수 밖에 없으며, upper layer인 RLP(혹은 RLC)에서는 이를 re-sequencing하여야 하는 부담감이 생기게 된다. 본 논문에서는 RLP receiver에서의 re-sequencing방법에 있어서, 효율적으로 RLP-NAK의 전송시점을 결정하는 NAK suppression 방법을 제안하고 있으며, 실험을 통하여 높은 성능향상을 보임을 확인할 수 있다.

• Korean Management Science Review
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• v.13 no.1
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• pp.13-27
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• 1996

This paper considers the sequencing problem in mixed model assembly lines with hybrid workstation types and sequence-dependent setup times. Computation time is often a critical factor in choosing a method of determining the sequence. We develop a mathematical formulation of the problem to minimize the overall length of a line, and present a tabu search technique which can provide a near optimal solution in real time. The proposed technique is compared with a genetic algorithm and a branch-and-bound method. Experimental results are reported to demonstrate the efficiency of the technique.

• Journal of Life Science
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• v.14 no.1
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• pp.26-31
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• 2004

Redox factor-1 (Ref-1), known as a redox regulator, controls the DNA binding of AP-1 and is activated in HT29 colon cancer cells by hypoxia in vitro. REF-1 also increases tile DNA binding affinity of Hypoxia-inducible Factor-lalpha$ (HIF-lalpha$), HIF-like Factor (HLF) and early growth response-1 (Egr-1) which induce expression of the genes involved in angiogenesis, so that we speculate that REF-1 may play a role in hypoxia-induced angiogenesis. In this research we tried to detect novel proteins interacting with REF-1 using Yeast two-hybrid system using full-length REF-1 cDNA as bait. As result of such screening we detected 3 positive clones. DNA sequencing and GeneBank search revealed that one of the clones contained the same sequences as M.musculus cDNA for tioredoxin.

• BMB Reports
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• v.50 no.4
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• pp.201-207
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• 2017

Alternations in usage of polyadenylation sites during transcription termination yield transcript isoforms from a gene. Recent findings of transcriptome-wide alternative polyadenylation (APA) as a molecular response to changes in biology position APA not only as a molecular event of early transcriptional termination but also as a cellular regulatory step affecting various biological pathways. With the development of high-throughput profiling technologies at a single nucleotide level and their applications targeted to the 3'-end of mRNAs, dynamics in the landscape of mRNA 3'-end is measureable at a global scale. In this review, methods and technologies that have been adopted to study APA events are discussed. In addition, various bioinformatics algorithms for APA isoform analysis using publicly available RNA-seq datasets are introduced.

• Transactions of the Korean Society of Machine Tool Engineers
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• v.14 no.5
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• pp.27-34
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• 2005

To accomplish various and complex tasks by intelligent robots, improvement is needed not only in mechanical system architecture but also in control system architecture. Hybrid control architecture has been suggested as a mutually complementing architecture of the weak points of a deliberative and a reactive control. This paper addresses a control architecture of robots, and a behavior representation methodology. The suggested control architecture consists of three layers of deliberative, sequencing, and reactive as hybrid control architecture. Multi-layer behavior model is employed to represent desired tasks. 3D simulation will be conducted to verify the applicability of suggested control architecture and behavior representation method.

• Journal of Aquaculture
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• v.10 no.4
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• pp.403-407
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• 1997

Intraspecific sequence variation was detected by polymerase chain reaction (PCR) and direct sequencing of a 350-nucleotide region of the mitochondrial 12S rRNA gene of two natural populations (Han River and Nakdong River) and one hatchery stock (Jinhae Inland Fisheries Institute) of local strain common carp, one Israeli strain of common carp stock from Pukyong National University (PKU), and one hybrid between Israeli strain of common carp female and local strain common carp male from PKU stock. There is little variation in 350 bases of the mitochondrial 12S rRNA gene sequences among 2 natural and 1 hatchery local strain common carp populatins, representing abut 7 to 20 nucleotide differences (less than 6%). The sequence of specimens from Han River was more similar to that from Nakdong River (identity=98.0%) than to that from Jinhae Inland Fisheries Institute (identity=96.3%). Sequence variation between Israeli strain and wild local strain common carp was higher than the variation within natural stocks. The level of variation was ranged from 15.7 to 17.7%. The hybrid showed very similar nucleotide4 sequence of 12S rRNA gene to the sequence of Israeli strain with the identity of 98.9%.

• Journal of Korean Society of Industrial and Systems Engineering
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• v.33 no.4
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• pp.58-68
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• 2010

Particle Swarm Optimization (PSO) which has been well known to solve continuous problems can be applied to discrete combinatorial problems. Several DPSO (Discrete Particle Swarm Optimization) algorithms have been proposed to solve discrete problems such as traveling salesman, vehicle routing, and flow shop scheduling problems. They are different in representation of position and velocity vectors, operation mechanisms for updating vectors. In this paper, the performance of 5 DPSOs is analyzed by applying to traditional Traveling Salesman Problems. The experiment shows that DPSOs are comparable or superior to a genetic algorithm (GA). Also, hybrid PSO combined with local optimization (i.e., 2-OPT) provides much improved solutions. Since DPSO requires more computation time compared with GA, however, the performance of hybrid DPSO is not better than hybrid GA.