• Journal of Communications and Networks
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• 제5권3호
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• pp.230-239
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• 2003

In this paper, we propose a framework to study how to route packets efficiently in multipath communication networks. Two traffic congestion control techniques, namely, flow assignment and packet scheduling, have been investigated. The flow assignment mechanism defines an optimal splitting of data traffic on multiple disjoint paths. The resequencing delay and the usage of the resequencing buffer can be reduced significantly by properly scheduling the sending order of all packets, say, according to their expected arrival times at the destination. To illustrate our model, and without loss of generality, Gaussian distributed end-to-end path delays are used. Our analytical results show that the techniques are very effective in reducing the average end-to-end path delay, the average packet resequencing delay, and the average resequencing buffer occupancy for various path configurations. These promising results can form a basis for designing future adaptive multipath protocols.

• 산업경영시스템학회지
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• 제32권3호
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• pp.118-126
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• 2009

This research investigates the problem of minimizing setup costs in resequencing jobs having first-in, first-out(FIFO) constraints at conveyorized production or assembly systems. Sequence changing at conveyor junctions in these systems is limited due to FIFO restriction. We first define the general problem of resequencing jobs to workstations satisfying precedence relationships between jobs(Generalized Sequential Ordering Problem, GSOP). Then we limit our scope to FIFO precedence relationships which is the conveyor selection problem at a diverging junction(Diverging Sequential Ordering Problem, DSOP), modeling it as a 0-1 integer program. With the capacity constraint removed, we show that the problem can be modeled as an assignment problem. In addition, we proposed and evaluated the heuristic algorithm for the case where the capacity constraint cannot be removed. Finally, we discuss the case study which motivated this research and numerical results.

• Journal of Plant Biotechnology
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• 제46권2호
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• pp.71-78
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• 2019

The objective of this study was to use 'Danta PR', NGS (Next Generation Sequencing) technology for genome resequencing to develop polymorphic makers between Chinese oriental melon, 'Hyangseo 1' and Korean oriental melon. From the resequencing data that covered about 81 times of the genome size, 104,357 of SSR motifs and Indel, and 1,092,436 of SNPs were identified. 299 SSR and 307 Indel markers were chosen to cover each chromosome with 25 markers. These markers were subsequently used to identify genotypes of 'Danta PR' BC1 (F1 x 'Danta PR') population and a genetic linkage map was constructed. SSR, Indel, and SNPs identified in this study would be useful as a breeding tool to develop new oriental melon varieties.

• 대한전자공학회논문지TC
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• 제41권9호
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• pp.73-80
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• 2004

본 논문에서는, 고성능 결함 감내 셀 스위치인, 사이클릭 벤얀 망의 셀 순서의 무결성 문제를 해결하기 위한 셀 재배열 버퍼를 제시한다. 사이클릭 벤얀 스위치는, 편향 자기 경로제어를 사용하여, 입력 정합과 출력 정합 사이에 다중 경로들을 제공함으로써, 높은 신뢰성을 제공하고, 스위치의 내부 링크들의 혼잡 문제를 해결한다. 그런데, 이러한 다중 경로들은 길이가 서로 다를 수 있다 따라서 셀들이 입력 정합에 도착한 순서와 다르게 출력 정합에 도달할 수 있다. 제안된 셀 재배열 버퍼는 이러한 셀 순서의 무결성 문제를 해결하는 일종의 하드웨어 슬라이딩 윈도우 메커니즘이다. 본 장치 구성의 주요 비용은 슬라이딩 윈도우를 구성하는 하드웨어 비용이다. 따라서 필요한 슬라이딩 윈도우의 크기를 계산하기 위해서, 비균일 주소 분포를 가진 트래픽 부하 하에서 스위치를 시뮬레이션하여, 셀들이 스위치를 통과할 때 발생하는 지연 분포를 분석을 하였다. 이 분석을 통하여, 적은 양의 범용 메모리와 제어 논리를 사용하여, 셀 순서의 무결성 문제를 해결하는 셀 재배열 버퍼를 만들 수 있다는 사실을 밝혔다. 본 논문에서 제시한 셀 재배열 버퍼는 다른 다중 경로 스위칭 망들을 위해서도 사용될 수 있다.

• Genomics & Informatics
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• 제8권3호
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• pp.131-137
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• 2010

Genome-wide association studies (GWASs) have greatly contributed to the identification of common variants responsible for numerous complex traits. There are, however, unavoidable limitations in detecting causal and/or rare variants for traits in this approach, which depends on an LD-based tagging SNP microarray chip. In an effort to detect potential casual and/or rare variants for complex traits, such as type 2 diabetes (T2D) and triglycerides (TGs), we conducted a targeted resequencing of loci identified by the Korea Association REsource (KARE) GWAS. The target regions for resequencing comprised whole exons, exon-intron boundaries, and regulatory regions of genes that appeared within 1 Mb of the GWA signal boundary. From 124 individuals selected in population-based cohorts, a total of 0.7 Mb target regions were captured by the NimbleGen sequence capture 385K array. Subsequent sequencing, carried out by the Roche 454 Genome Sequencer FLX, generated about 110,000 sequence reads per individual. Mapping of sequence reads to the human reference genome was performed using the SSAHA2 program. An average of 62.2% of total reads was mapped to targets with an average 22X-fold coverage. A total of 5,983 SNPs (average 846 SNPs per individual) were called and annotated by GATK software, with 96.5% accuracy that was estimated by comparison with Affymetrix 5.0 genotyped data in identical individuals. About 51% of total SNPs were singletons that can be considered possible rare variants in the population. Among SNPs that appeared in exons, which occupies about 20% of total SNPs, 304 nonsynonymous singletons were tested with Polyphen to predict the protein damage caused by mutation. In total, we were able to detect 9 and 6 potentially functional rare SNPs for T2D and triglycerides, respectively, evoking a further step of replication genotyping in independent populations to prove their bona fide relevance to traits.

• 한국임상수의학회지
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• 제36권4호
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• pp.190-195
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• 2019

We aimed to identify genomic variations as well as the marker genes related with chronic mitral valve disease (CMVD) in Canis lupus familiaris using whole genome resequencing, which provides valuable resources for further study. Two ten-year old female Canis lupus familiaris English cocker spaniels were used for this study, one control and one who had been diagnosed as CMVD. For the whole genome resequencing, muscles from the left ventricular wall were collected from each dog. With the HiSeq DNA Shotgun library and $HiSeq^{TM}$ 2000 platform, whole genome resequencing was performed. From the results, we identified 5 million and 6 million variants in gene expression in the control and CMVD-diagnosed subject, respectively. We then selected the top 1,000 genes from the SNP, INS, and DEL mutation and 675 genes among them were overlapped for every mutation between the control and CMVD-diagnosed patient. Interestingly, in both groups, the intron variant (91.16 and 91.18%) and upstream variant (3.10 and 3.08%) are most highly related. Among the overlapped 675 genes, gene ontology for intracellular signal transduction is highly counted in INS, and DEL, and SNPs (35, 33, 31, respectively). In this study, we found that the COL and CDH gene families could be key molecules in identifying the difference in gene expression between control and CMVD-diagnosed dogs. We believe further studies will prove the importance of variants in key molecule expression and that these data will serve as a valuable foundation stone the study of canine CMVD.

• Journal of Plant Biotechnology
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• 제45권3호
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• pp.228-235
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• 2018

In this study, two pepper varieties, PRH1 (powdery mildew resistance line) and Saengryeg (powdery mildew resistance line), were resequenced using next generation sequencing technology in order to develop InDel markers. The genome-wide discovery of InDel variation was performed by comparing the whole-genome resequencing data of two pepper varieties to the Capsicum annuum cv. CM334 reference genome. A total of 334,236 and 318,256 InDels were identified in PRH1 and Saengryeg, respectively. The greatest number of homozygous InDels were discovered on chromosome 1 in PRH1 (24,954) and on chromosome 10 (29,552) in Saengryeg. Among these homozygous InDels, 19,094 and 4,885 InDels were distributed in the genic regions of PRH1 and Saengryeg, respectively, and 198,570 and 183,468 InDels were distributed in the intergenic regions. We have identified 197,821 polymorphic InDels between PRH1 and Saengryeg. A total of 11,697 primers sets were generated, resulting in the discovery of four polymorphic InDel markers. These new markers will be utilized in order to identify disease resistance genotypes in breeding populations. Therefore, our results will make a one-step advancement in whole genome resequencing and add genetic resource datasets in pepper breeding research.

• 유전체소식지
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• 제11권1호
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• pp.17-20
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• 2011

• Genomics & Informatics
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• 제6권2호
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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.

• 한국축산식품학회지
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• 제33권6호
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• pp.715-722
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• 2013

Heugu (Korea Black Cattle) is one of the indigenous cattle breeds in Korea; however there has been severe lack of genomic studies on the breed. In this study, we report the first whole genome resequencing of Heugu at higher sequence coverage using Illumina HiSeq 2000 platform. More than 153.6 Giga base pairs sequence was obtained, of which 97% of the reads were mapped to the bovine reference sequence assembly (UMD 3.1). The number of non-redundantly mapped sequence reads corresponds to approximately 28.9-fold coverage across the genome. From these data, we identified a total of over six million single nucleotide polymorphisms (SNPs), of which 29.4% were found to be novel using the single nucleotide polymorphism database build 137. Extensive annotation was performed on all the detected SNPs, showing that most of SNPs were located in intergenic regions (70.7%), which is well corresponded with previous studies. Of the total SNPs, we identified substantial numbers of non-synonymous SNPs (13,979) in 5,999 genes, which could potentially affect meat quality traits in cattle. These results provide genome-wide SNPs that can serve as useful genetic tools and as candidates in searches for phenotype-altering DNA difference implicated with meat quality traits in cattle. The importance of this study can be further pronounced with the first whole genome sequencing of the valuable local genetic resource to be used in further genomic comparison studies with diverse cattle breeds.