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Relevant bibliographies by topics / Genome sequence assembly

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Academic literature on the topic 'Genome sequence assembly'

Author: Grafiati

Published: 4 June 2021

Last updated: 11 February 2022

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Journal articles on the topic "Genome sequence assembly"

1

Taylor, D. Leland, A. Malcolm Campbell, and Laurie J. Heyer. "Illuminating the Black Box of Genome Sequence Assembly." American Biology Teacher 75, no. 8 (October 1, 2013): 572–77. http://dx.doi.org/10.1525/abt.2013.75.8.9.

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Next-generation sequencing technologies have greatly reduced the cost of sequencing genomes. With the current sequencing technology, a genome is broken into fragments and sequenced, producing millions of “reads.” A computer algorithm pieces these reads together in the genome assembly process. PHAST is a set of online modules (http://gcat.davidson.edu/phast) designed to teach advanced high school and college students the genome assembly process. PHAST allows users to assemble phage genomes in real time and includes tutorials detailing the complexities of genome assembly. With PHAST, students learn concepts behind genome assembly and understand how mathematics solves biological problems such as genome assembly.

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Udall, Joshua A., Evan Long, Chris Hanson, Daojun Yuan, Thiruvarangan Ramaraj, Justin L. Conover, Lei Gong, et al. "De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri." G3: Genes|Genomes|Genetics 9, no. 10 (August 28, 2019): 3079–85. http://dx.doi.org/10.1534/g3.119.400392.

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Cotton is an agriculturally important crop. Because of its importance, a genome sequence of a diploid cotton species (Gossypium raimondii, D-genome) was first assembled using Sanger sequencing data in 2012. Improvements to DNA sequencing technology have improved accuracy and correctness of assembled genome sequences. Here we report a new de novo genome assembly of G. raimondii and its close relative G. turneri. The two genomes were assembled to a chromosome level using PacBio long-read technology, HiC, and Bionano optical mapping. This report corrects some minor assembly errors found in the Sanger assembly of G. raimondii. We also compare the genome sequences of these two species for gene composition, repetitive element composition, and collinearity. Most of the identified structural rearrangements between these two species are due to intra-chromosomal inversions. More inversions were found in the G. turneri genome sequence than the G. raimondii genome sequence. These findings and updates to the D-genome sequence will improve accuracy and translation of genomics to cotton breeding and genetics.

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Ghosh, Tarini Shankar, Varun Mehra, and Sharmila S. Mande. "Grid-Assembly: An oligonucleotide composition-based partitioning strategy to aid metagenomic sequence assembly." Journal of Bioinformatics and Computational Biology 13, no. 03 (May 15, 2015): 1541004. http://dx.doi.org/10.1142/s0219720015410048.

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Metagenomics approach involves extraction, sequencing and characterization of the genomic content of entire community of microbes present in a given environment. In contrast to genomic data, accurate assembly of metagenomic sequences is a challenging task. Given the huge volume and the diverse taxonomic origin of metagenomic sequences, direct application of single genome assembly methods on metagenomes are likely to not only lead to an immense increase in requirements of computational infrastructure, but also result in the formation of chimeric contigs. A strategy to address the above challenge would be to partition metagenomic sequence datasets into clusters and assemble separately the sequences in individual clusters using any single-genome assembly method. The current study presents such an approach that uses tetranucleotide usage patterns to first represent sequences as points in a three dimensional (3D) space. The 3D space is subsequently partitioned into "Grids". Sequences within overlapping grids are then progressively assembled using any available assembler. We demonstrate the applicability of the current Grid-Assembly method using various categories of assemblers as well as different simulated metagenomic datasets. Validation results indicate that the Grid-Assembly approach helps in improving the overall quality of assembly, in terms of the purity and volume of the assembled contigs.

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Collins, Andrew. "The Challenge of Genome Sequence Assembly." Open Bioinformatics Journal 11, no. 1 (October 17, 2018): 231–39. http://dx.doi.org/10.2174/1875036201811010231.

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Background: Although whole genome sequencing is enabling numerous advances in many fields achieving complete chromosome-level sequence assemblies for diverse species presents difficulties. The problems in part reflect the limitations of current sequencing technologies. Chromosome assembly from ‘short read’ sequence data is confounded by the presence of repetitive genome regions with numerous similar sequence tracts which cannot be accurately positioned in the assembled sequence. Longer sequence reads often have higher error rates and may still be too short to span the larger gaps between contigs. Objective: Given the emergence of exciting new applications using sequencing technology, such as the Earth BioGenome Project, it is necessary to further develop and apply a range of strategies to achieve robust chromosome-level sequence assembly. Reviewed here are a range of methods to enhance assembly which include the use of cross-species synteny to understand relationships between sequence contigs, the development of independent genetic and/or physical scaffold maps as frameworks for assembly (for example, radiation hybrid, optical motif and chromatin interaction maps) and the use of patterns of linkage disequilibrium to help position, orient and locate contigs. Results and Conclusion: A range of methods exist which might be further developed to facilitate cost-effective large-scale sequence assembly for diverse species. A combination of strategies is required to best assemble sequence data into chromosome-level assemblies. There are a number of routes towards the development of maps which span chromosomes (including physical, genetic and linkage disequilibrium maps) and construction of these whole chromosome maps greatly facilitates the ordering and orientation of sequence contigs.

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Sharma, Priyanka, Othman Al-Dossary, Bader Alsubaie, Ibrahim Al-Mssallem, Onkar Nath, Neena Mitter, Gabriel Rodrigues Alves Margarido, et al. "Improvements in the sequencing and assembly of plant genomes." Gigabyte 2021 (June 4, 2021): 1–10. http://dx.doi.org/10.46471/gigabyte.24.

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Advances in DNA sequencing have made it easier to sequence and assemble plant genomes. Here, we extend an earlier study, and compare recent methods for long read sequencing and assembly. Updated Oxford Nanopore Technology software improved assemblies. Using more accurate sequences produced by repeated sequencing of the same molecule (Pacific Biosciences HiFi) resulted in less fragmented assembly of sequencing reads. Using data for increased genome coverage resulted in longer contigs, but reduced total assembly length and improved genome completeness. The original model species, Macadamia jansenii, was also compared with three other Macadamia species, as well as avocado (Persea americana) and jojoba (Simmondsia chinensis). In these angiosperms, increasing sequence data volumes caused a linear increase in contig size, decreased assembly length and further improved already high completeness. Differences in genome size and sequence complexity influenced the success of assembly. Advances in long read sequencing technology continue to improve plant genome sequencing and assembly. However, results were improved by greater genome coverage, with the amount needed to achieve a particular level of assembly being species dependent.

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Jackman, Shaun D., Lauren Coombe, René L. Warren, Heather Kirk, Eva Trinh, Tina MacLeod, Stephen Pleasance, et al. "Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure." Genome Biology and Evolution 12, no. 7 (May 25, 2020): 1174–79. http://dx.doi.org/10.1093/gbe/evaa108.

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Abstract Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the complete 5.5-Mb mitochondrial genome of Sitka spruce (Picea sitchensis), to date, one of the largest mitochondrial genomes of a gymnosperm. We sequenced the whole genome using Oxford Nanopore MinION, and then identified contigs of mitochondrial origin assembled from these long reads based on sequence homology to the white spruce mitochondrial genome. The assembly graph shows a multipartite genome structure, composed of one smaller 168-kb circular segment of DNA, and a larger 5.4-Mb single component with a branching structure. The assembly graph gives insight into a putative complex physical genome structure, and its branching points may represent active sites of recombination.

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Rihtman, Branko, Sean Meaden, Martha R. J. Clokie, Britt Koskella, and Andrew D. Millard. "Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes." PeerJ 4 (June 1, 2016): e2055. http://dx.doi.org/10.7717/peerj.2055.

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Bacteriophages are the most abundant biological entities on the planet, playing crucial roles in the shaping of bacterial populations. Phages have smaller genomes than their bacterial hosts, yet there are currently fewer fully sequenced phage than bacterial genomes. We assessed the suitability of Illumina technology for high-throughput sequencing and subsequent assembly of phage genomes. In silico datasets reveal that 30× coverage is sufficient to correctly assemble the complete genome of ˜98.5% of known phages, with experimental data confirming that the majority of phage genomes can be assembled at 30× coverage. Furthermore, in silico data demonstrate it is possible to co-sequence multiple phages from different hosts, without introducing assembly errors.

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Tanaka, Mami, Sayaka Mino, Yoshitoshi Ogura, Tetsuya Hayashi, and Tomoo Sawabe. "Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case." PeerJ 6 (June 18, 2018): e5018. http://dx.doi.org/10.7717/peerj.5018.

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Whole genome sequence comparisons have become essential for establishing a robust scheme in bacterial taxonomy. To generalize this genome-based taxonomy, fast, reliable, and cost-effective genome sequencing methodologies are required. MinION, the palm-sized sequencer from Oxford Nanopore Technologies, enables rapid sequencing of bacterial genomes using minimal laboratory resources. Here we tested the ability of Nanopore sequences for the genome-based taxonomy of Vibrionaceae and compared Nanopore-only assemblies to complete genomes of five Rumoiensis clade species: Vibrio aphrogenes, V. algivorus, V. casei, V. litoralis, and V. rumoiensis. Comparison of overall genome relatedness indices (OGRI) and multilocus sequence analysis (MLSA) based on Nanopore-only assembly and Illumina or hybrid assemblies revealed that errors in Nanopore-only assembly do not influence average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), G+C content, or MLSA tree topology in Vibrionaceae. Our results show that the genome sequences from Nanopore-based approach can be used for rapid species identification based on the OGRI and MLSA.

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Mascher, Martin, Thomas Wicker, Jerry Jenkins, Christopher Plott, Thomas Lux, Chu Shin Koh, Jennifer Ens, et al. "Long-read sequence assembly: a technical evaluation in barley." Plant Cell 33, no. 6 (March 12, 2021): 1888–906. http://dx.doi.org/10.1093/plcell/koab077.

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Abstract Sequence assembly of large and repeat-rich plant genomes has been challenging, requiring substantial computational resources and often several complementary sequence assembly and genome mapping approaches. The recent development of fast and accurate long-read sequencing by circular consensus sequencing (CCS) on the PacBio platform may greatly increase the scope of plant pan-genome projects. Here, we compare current long-read sequencing platforms regarding their ability to rapidly generate contiguous sequence assemblies in pan-genome studies of barley (Hordeum vulgare). Most long-read assemblies are clearly superior to the current barley reference sequence based on short-reads. Assemblies derived from accurate long reads excel in most metrics, but the CCS approach was the most cost-effective strategy for assembling tens of barley genomes. A downsampling analysis indicated that 20-fold CCS coverage can yield very good sequence assemblies, while even five-fold CCS data may capture the complete sequence of most genes. We present an updated reference genome assembly for barley with near-complete representation of the repeat-rich intergenic space. Long-read assembly can underpin the construction of accurate and complete sequences of multiple genomes of a species to build pan-genome infrastructures in Triticeae crops and their wild relatives.

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Buza, Krisztian, Bartek Wilczynski, and Norbert Dojer. "RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes." International Journal of Genomics 2015 (2015): 1–10. http://dx.doi.org/10.1155/2015/563482.

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Background. Next-generation sequencing technologies are now producing multiple times the genome size in total reads from a single experiment. This is enough information to reconstruct at least some of the differences between the individual genome studied in the experiment and the reference genome of the species. However, in most typical protocols, this information is disregarded and the reference genome is used.Results. We provide a new approach that allows researchers to reconstruct genomes very closely related to the reference genome (e.g., mutants of the same species) directly from the reads used in the experiment. Our approach applies de novo assembly software to experimental reads and so-called pseudoreads and uses the resulting contigs to generate a modified reference sequence. In this way, it can very quickly, and at no additional sequencing cost, generate new, modified reference sequence that is closer to the actual sequenced genome and has a full coverage. In this paper, we describe our approach and test its implementation called RECORD. We evaluate RECORD on both simulated and real data. We made our software publicly available on sourceforge.Conclusion. Our tests show that on closely related sequences RECORD outperforms more general assisted-assembly software.

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Dissertations / Theses on the topic "Genome sequence assembly"

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Nasser, Sara. "Fuzzy methods for meta-genome sequence classification and assembly." abstract and full text PDF (free order & download UNR users only), 2008. http://0-gateway.proquest.com.innopac.library.unr.edu/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3307706.

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Freeman, Alex J. "The Genome Sequence of Gossypium herbaceum (A1), a Domesticated Diploid Cotton." BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/7329.

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Gossypium herbaceum is a species of cotton native to Africa and Asia. As part of a larger effort to investigate structural variation in assorted diploid and polyploid cotton genomes we have sequenced and assembled the genome of G. herbaceum. Cultivated G. herbaceum is an A1-genome diploid from the Old World (Africa) with a genome size of approximately 1.7 Gb. Long range information is essential in constructing a high-quality assembly, especially when the genome is expected to be highly repetitive. Here we present a quality draft genome of G. herbaceum (cv. Wagad) using a multi-platform sequencing strategy (PacBio RS II, Dovetail Genomics, Phase Genomics, BioNano Genomics). PacBio RS II (60X) long reads were de novo assembled using the CANU assembler. Illumina sequence reads generated from the PROXIMO library method from Phase Genomics, and BioNano high-fidelity whole genome maps were used to further scaffolding. Finally, the assembly was polished using PILON. This multi-platform long range sequencing strategy will help greatly in attaining high quality de novo reconstructions of genomes. This assembly will be used towards comparative analysis with G. arboreum, which is also a domesticated A2-genome diploid. Not only will this provide a quality reference genome for G. herbaceum, it also provides an opportunity to assess recent technologies such as Dovetail Genomics, Phase Genomics, and Bionano Genomics. The G. herbaceum genome sequence serves as an example to the plant genomics community for those who have an interest in using multi-platform sequencing technologies for de novo genome sequencing.

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Lee, Rebekah Ann. "Assembly, Annotation and Optical Mapping of the A Subgenome of Avena." BYU ScholarsArchive, 2017. https://scholarsarchive.byu.edu/etd/7238.

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Common oat (Avena) has held a significant place within the global crop community for centuries; although its cultivation has decreased over the past century, its nutritional benefits have recently garnered increased interest for human consumption. No published reference sequences are available for any of the three oat subgenomes. Here we report a quality sequence assembly, annotation and hybrid optical map of the A-genome diploid Avena atlantica Baum and Fedak. The assembly is composed of a total of 3,417 contigs with an N50 of 11.86 Mb and an estimated completeness of 97.6%. This genome sequence will be a valuable research tool within the oat community.

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Bodily, Paul Mark. "Inverted Sequence Identification in Diploid Genomic Scaffold Assembly via Weighted MAX-CUT Reduction." BYU ScholarsArchive, 2013. https://scholarsarchive.byu.edu/etd/3793.

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Virtually all genome assemblers to date are designed for use with data from haploid or homozygous diploid genomes. Their use on heterozygous genomic datasets generally results in highly-fragmented, error-prone assemblies, owing to the violation of assumptions during both the contigging and scaffolding phases. Of the two phases, scaffolding is more particularly impacted and algorithms to facilitate the scaffolding of heterozygous data are lacking. We present a stand-alone scaffolding algorithm, ScaffoldScaffolder, designed specifically for scaffolding diploid genomes. A fundamental step in the scaffolding phase is the assignment of sequence orientations to contigs within scaffolds. Deciding such an assignment in the presence of ambiguous evidence is what is termed the contig orientation problem. We define this problem using bidirected graph theory and show that it is equivalent to the weighted MAX-CUT problem. We present a greedy heuristic solution which we comparatively assess with other solutions to the contig orientation problem, including an advanced MAX-CUT heuristic. We illustrate how a solution to this problem provides a simple means of simultaneously identifying inverted haplotypes, which are uniquely found in diploid genomes and which have been shown to be involved in the genetic mechanisms of several diseases. Ultimately our findings show that due to the inherent biases in the underlying biological model, a greedy heuristic algorithm performs very well in practice, retaining a higher total percent of edge weight than a branch-and-bound semidefinite programming heuristic. This application exemplifies how existing graph theory algorithms can be applied in the development of new algorithms for more accurate assembly of heterozygous diploid genomes.

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Sharp, Aaron Robert. "Improving Cotton Agronomics with Diverse Genomic Technologies." BYU ScholarsArchive, 2016. https://scholarsarchive.byu.edu/etd/5845.

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Agronomic outcomes are the product of a plant's genotype and its environment. Genomic technologies allow farmers and researchers new avenues to explore the genetic component of agriculture. These technologies can also enhance understanding of environmental effects. With a growing world population, a wide variety of tools will be necessary to increase the agronomic productivity. Here I use massively parallel, deep sequencing of RNA (RNA-Seq) to measure changes in cotton gene expression levels in response to a change in the plant's surroundings caused by conservation tillage. Conservation tillage is an environmentally friendly, agricultural practice characterized by little or no inversion of the soil prior to planting. In addition to changes in cotton gene expression and biological pathway activity, I assay the transcriptional activity of microbial symbiotes living in and around the cotton roots. I found a large degree of similarity between cotton individuals in different treatments. However, under conventional disk tillage I did find significantly greater activity of cotton phosphatase and sulfate transport genes, as well as greater abundance of the microbes Candidatus Burkholderia brachynathoides and Arthrobacter species L77. This study also includes the use of high-throughput physical mapping of DNA to examine the genomic structure of a wild cotton species, Gossypium raimondii, which is closely related to the economically significant crop species Gossypium hirsutum. This technology characterizes genomic regions by assembling large input DNA molecules labeled at restriction enzyme recognition sites. I created an efficient algorithm and generated 812 whole genome assemblies from two datasets. The best of these assemblies allowed us to detect 3,806 potential misassemblies in the current release of the G. raimondii genome sequence assembly.

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Childers, Christopher P. "Sequence assembly and annotation of the bovine major histocompatibility complex (BoLA) class IIb region, and in silico detection of sequence polymorphisms in BoLA IIb." Texas A&M University, 2006. http://hdl.handle.net/1969.1/4821.

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Cattle are vitally important to American agriculture industry, generating over 24.6 billion pounds of beef (by carcass weight), and 79.5 billion dollars in 2005, and over 27 billion dollars in milk sales in 2004. As of July 2006, the U.S. beef and dairy industry is comprised of 104.5 million head of cattle, 32.4 million of which were processed in 2005. The health of the animals has always been an important concern for breeders, as healthy animals grow faster and are more likely to reach market weight. Animals that exhibit natural resistance to disease do not require chemicals to stimulate normal weight gain, and are less prone to disease related wasting. The major histocompatibility complex (MHC) is a collection of genes, many of which function in antigen processing and presentation. The bovine MHC (BoLA) differs from typical mammalian MHCs in that the class II region was disrupted by a chromosomal inversion into two subregions, designated BoLA IIa and BoLA IIb. BoLA IIb was transposed to a position near the centromere on bovine chromosome 23,while BoLA IIa retains its position in BoLA. Comparative sequence analysis of BoLA IIb with the human MHC revealed the location of the region containing the proximal inversion breakpoint. Gene content, order and orientation of BoLA IIb are consistent with the single inversion hypothesis when compared to the corresponding region of the human class II MHC (HLA class II). BoLA IIb spans approximately 450 kb. The genomic sequence of BoLA IIb was used to detect sequence variation through comparison to other bovine sequences, including data from the bovine genome project, and two regions in the BAC scaffold used to develop the BoLA IIb sequence. Analysis of the bovine genome project sequence revealed a total of 10,408 mismatching bases, 30 out of 231 polymorphic microsatellites, and 15 sequences corresponding to the validated SNP panel generated by the bovine genome sequencing project. The two overlapping regions in the BoLA IIb BAC scaffold were found to have 888 polymorphisms, including a total of 6 out of 42 polymorphic microsatellites indicating that each BAC derived from a different chromosome.

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Savel, Daniel M. "Towards a Human Genomic Coevolution Network." Case Western Reserve University School of Graduate Studies / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=case1524241451267546.

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Jäger, Sarah Christina [Verfasser]. "Hybrid Assembly of Whole Genome Shotgun Sequences of Two Sugar Beet (Beta vulgaris L.) Translocation Lines Carrying the Beet Cyst Nematode Resistance Gene Hs1-2 and Functional Analysis of Candidate Genes / Sarah Christina Jäger." Kiel : Universitätsbibliothek Kiel, 2013. http://d-nb.info/1054661898/34.

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Huang, Chih-Chang, and 黃至昶. "Establishing a Computational Pipeline of Genome Projects: Sequence Assembly, Gene Annotation and Metabolic Pathway Reconstruction." Thesis, 2010. http://ndltd.ncl.edu.tw/handle/30090000954245955675.

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碩士
國立交通大學
生物資訊及系統生物研究所
98
Human Genome Project had been completed in 2003. It provides gigantic resources for biological research. In recent years, next generation sequencing technique dramatically reduces the sequencing cost and time. Thus, completely sequencing new organisms will be popular and universal, and the genomes of these organisms also include huge research resources. The demands of comprehensive genomic annotation will be more urgent and necessary. Thus, it is necessary a computational pipeline. In order to assembly complete genome sequences, this pipeline uses several assembly tools which designed for assembling traditional sequencing and next generate sequencing raw data. It also integrates ab initio and evidence-based gene prediction approaches to predict genes. In addition, this pipeline can reconstruct metabolic pathways from the gene annotation results. This computational pipeline can assemble sequencing data from various platforms and provide the service of genomic annotation including: gene annotation and metabolic pathway reconstruction. This computational pipeline can be a crucial part of pipeline in the high throughput genomic annotation.

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Andere, Anne A. "De novo genome assembly of the blow fly Phormia regina (Diptera: Calliphoridae)." Thesis, 2014. http://hdl.handle.net/1805/5630.

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Indiana University-Purdue University Indianapolis (IUPUI)
Phormia regina (Meigen), commonly known as the black blow fly is a dipteran that belongs to the family Calliphoridae. Calliphorids play an important role in various research fields including ecology, medical studies, veterinary and forensic sciences. P. regina, a non-model organism, is one of the most common forensically relevant insects in North America and is typically used to assist in estimating postmortem intervals (PMI). To better understand the roles P. regina plays in the numerous research fields, we re-constructed its genome using next generation sequencing technologies. The focus was on generating a reference genome through de novo assembly of high-throughput short read sequences. Following assembly, genetic markers were identified in the form of microsatellites and single nucleotide polymorphisms (SNPs) to aid in future population genetic surveys of P. regina. A total 530 million 100 bp paired-end reads were obtained from five pooled male and female P. regina flies using the Illumina HiSeq2000 sequencing platform. A 524 Mbp draft genome was assembled using both sexes with 11,037 predicted genes. The draft reference genome assembled from this study provides an important resource for investigating the genetic diversity that exists between and among blow fly species; and empowers the understanding of their genetic basis in terms of adaptations, population structure and evolution. The genomic tools will facilitate the analysis of genome-wide studies using modern genomic techniques to boost a refined understanding of the evolutionary processes underlying genomic evolution between blow flies and other insect species.

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Book chapters on the topic "Genome sequence assembly"

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Nasser, Sara, Adrienne Breland, Frederick C. Harris, Monica Nicolescu, and Gregory L. Vert. "Fuzzy Genome Sequence Assembly for Single and Environmental Genomes." In Fuzzy Systems in Bioinformatics and Computational Biology, 19–44. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-540-89968-6_2.

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Wade, Claire M. "Assembly and Analysis of the Equine Genome Sequence." In Equine Genomics, 103–11. Oxford, UK: Blackwell Publishing Ltd., 2013. http://dx.doi.org/10.1002/9781118522158.ch6.

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Stein, Nils, and Martin Mascher. "Barley Genome Sequencing and Assembly—A First Version Reference Sequence." In Compendium of Plant Genomes, 57–71. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-92528-8_5.

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Joets, Johann, Clémentine Vitte, and Alain Charcosset. "Draft Assembly of the F2 European Maize Genome Sequence and Its Comparison to the B73 Genome Sequence: A Characterization of Genotype-Specific Regions." In Compendium of Plant Genomes, 3–12. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-97427-9_1.

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Nowak, Robert M. "Genome Assembler for Repetitive Sequences." In Information Technologies in Biomedicine, 422–29. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-31196-3_42.

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Tang, Jun, Dong Huang, Chen Wang, Wei Wang, and Baile Shi. "GiSA: A Grid System for Genome Sequences Assembly." In Lecture Notes in Computer Science, 831–33. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-30464-7_63.

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Dlugosch, Katrina M., and Aurélie Bonin. "Allele Identification in Assembled Genomic Sequence Datasets." In Data Production and Analysis in Population Genomics, 197–211. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-61779-870-2_12.

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Anantharaman, Thomas, and Bud Mishra. "False Positives in Genomic Map Assembly and Sequence Validation." In Lecture Notes in Computer Science, 27–40. Berlin, Heidelberg: Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/3-540-44696-6_3.

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Hahn, Christoph. "Assembly of Ancient Mitochondrial Genomes Without a Closely Related Reference Sequence." In Methods in Molecular Biology, 195–213. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9176-1_18.

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Ning, Li, Xiaozhu Wang, and Zhanjiang Liu. "Next-Generation Sequencing Technologies and the Assembly of Short Reads into Reference Genome Sequences." In Bioinformatics in Aquaculture, 43–73. Chichester, UK: John Wiley & Sons, Ltd, 2017. http://dx.doi.org/10.1002/9781118782392.ch3.

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Conference papers on the topic "Genome sequence assembly"

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Warnke-Sommer, Julia, Ishwor Thapa, and Hesham Ali. "Next generation sequence assembler mis-assembly of phage genomes with terminal redundancy." In 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2015. http://dx.doi.org/10.1109/bibm.2015.7359836.

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Sadler, J. Evan. "THE MOLECULAR BIOLOGY OF VON WILLEBRAND FACTOR." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643930.

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Human von Willebrand factor (vWF) is a plasma glycoprotein that is synthesized by endothelial cells and megakaryocytes, and perhaps by syncytiotrophoblast of placenta. The biosynthesis of vWF is very complex, involving proteolytic processing, glycosyla-tion, disulfide bond formation, and sulfation. Mature vWF consists of a single subunit of ∼ 250,000 daltons that is assembled into multimer ranging from dimers to species of over 10 million daltons. vWF performs its essential hemostatic function through several binding interactions, forming a bridge between specific receptors on the platelet surface and components of damaged vascular subendothelial connective tissue. Inherited deficiency of vWF, or von Willebrand disease (vWD), is the most common genetically transmitted bleeding disorder worldwide. The last two years has been a time of very rapid progress in understanding the molecular biology of vWF. Four research groups have independently isolated and sequenced the 9 kilobase full-length vWF cDNA. The predicted protein sequence has provided a foundation for understanding the biosynthetic processing of vWF, and has clarified the relationship between vWF and a 75-100 kilodalton plasma protein of unknown function, von Willebrand antigen II (vWAgll)/ vWAgll is co-distributed with vWF in endothelial cells and platelets, and is deficient in patients with vWD. The cDNA sequence of vWF shows that vWAgll is a rather large pro-peptide for vWF, explaining the biochemical and genetic association between the two proteins. vWF has a complex evolutionary history marked by many separate gene segment duplications. The primary structure of the protein contains four distinct types of repeated domains present in two to four copies each. Repeated domains account for over 90 percent of the protein sequence. This sequence provides a framework for ordering the functional domains that have been defined by protein chemistry methods. A tryptic peptide from the amino-terminus of vWF that overlaps domain D3 binds to factor VIII and also appears to bind to heparin. Peptides that include domain A1 bind to collagens, to heparin, and to platelet glycoprotein Ib. A second collagen binding site appears to lie within domain A3. The vWF cDNA has been expressed in heterologous cells to produce small amounts of functionally and structurally normal vWF, indicating that endothelial cells are not unique in their ability to process and assemble vWF multimers. Site-directed mutagenesis has been used to show that deletion of the propeptide of vWF prevents the formation of multimers. Cloned cDNA probes have been employed to isolate vWF genomic DNA from cosmid and λ-phage libraries, and the size of the vWF gene appears to be ∼ 150 kilobases. The vWF locus has been localized to human chromosome 12p12—pter. Several intragenic RFLPs have been characterized. With them, vWF has been placed on the human genetic linkage map as the most telomeric marker currently available for the short arm of chromosome 12. A second apparently homologous locus has been identified on chromosome 22, but the relationship of this locus to the authentic vWF gene is not yet known. The mechanism of vWD has been studied by Southern blotting of genomic DNA with cDNA probes in a few patients. Three unrelated pedigrees have been shown to have total deletions of the vWF gene as the cause of severe vWD (type III). This form of gene deletion appears to predispose to the development of inhibitory alloantibodies to vWF during therapy with cryoprecipitate. During the next several years recombinant DNA methods will continue to contribute our understanding of the evolution, biosynthesis, and structure-function relationships of vWF, as well as the mechanism of additional variants of vWD at the level of gene structure.

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Nasser, Sara, Gregory L. Vert, Adrienne Breland, and Monica Nicolescu. "Fuzzy Classification of Genome Sequences Prior to Assembly Based on Similarity Measures." In NAFIPS 2007 - 2007 Annual Meeting of the North American Fuzzy Information Processing Society. IEEE, 2007. http://dx.doi.org/10.1109/nafips.2007.383864.

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Ye, Lu, and JingYang Gao. "Integrated Sequence Assembly-based Approach for Calling Genomic Long Insertion." In 2017 2nd International Conference on Automation, Mechanical Control and Computational Engineering (AMCCE 2017). Paris, France: Atlantis Press, 2017. http://dx.doi.org/10.2991/amcce-17.2017.147.

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Duan, Xiaohui, Kun Zhao, and Weiguo Liu. "HiPGA: A High Performance Genome Assembler for Short Read Sequence Data." In 2014 IEEE International Parallel & Distributed Processing Symposium Workshops (IPDPSW). IEEE, 2014. http://dx.doi.org/10.1109/ipdpsw.2014.68.

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Shen, Xiaohu, and Haris Vikalo. "A message passing algorithm for reference-guided sequence assembly from high-throughput sequencing data." In 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS). IEEE, 2012. http://dx.doi.org/10.1109/gensips.2012.6507720.

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Kang, Xiaojun, Shanyu Tang, Yongge Ma, Ruixiang Liu, and Yaping Wang. "De Bruijn Graph-Based Whole-Genomic Sequence Assembly Algorithms and Applications." In 2013 IEEE International Conference on Green Computing and Communications (GreenCom) and IEEE Internet of Things(iThings) and IEEE Cyber, Physical and Social Computing(CPSCom). IEEE, 2013. http://dx.doi.org/10.1109/greencom-ithings-cpscom.2013.393.

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Lugo, Wilfredo, and Jaime Seguel. "A fast and accurate parallel algorithm for genome mapping assembly aimed at massively parallel sequencers." In BCB '15: ACM International Conference on Bioinformatics, Computational Biology and Biomedicine. New York, NY, USA: ACM, 2015. http://dx.doi.org/10.1145/2808719.2812220.

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Ren, Z. F. "Nano Materials and Physics." In ASME 4th Integrated Nanosystems Conference. ASMEDC, 2005. http://dx.doi.org/10.1115/nano2005-87045.

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Aligning carbon nanotubes in any way desired is very important for many fundamental and applied research projects. In this talk, I will first discuss how to grow them with controlled diameter, length, spacing, and periodicity using catalyst prepared by magnetron sputtering, electron beam (e-beam) lithography, electrochemical deposition, and nanosphere self-assembly. Then I will present our results of field emission property of both the aligned carbon nanotubes grown on flat substrates and random carbon nanotubes grown on carbon cloth. For the aligned carbon nanotubes arrays, I will present the preliminary results of using them as photonic band gap crystals and nanoantennae. As an alternative material of carbon nanotubes, ZnO nanowires have been grown in both aligned fashion on flat substrates and random fashion on carbon cloth. Using these ZnO nanowires, good field emission properties were observed. Furthermore, I will present our recent studies on the electrical breakdown and transport properties of a single suspended nanotube grown on carbon cloth by a scanning electron microscope probe incorporated into a high resolution transmission electron microscope. As part of the potential applications, I will also discuss our recent success on molecules delivery into cells using carbon nanotubes. Finally I will talk about our most recent endeavor on achieving thermoelectric figure-of-merit (ZT) higher than 2 using our unique nanocomposite approach. Plasma-enhanced chemical vapor deposition (PECVD) was discovered by my group in 1998 to be able to grow aligned carbon nanotubes [1]. Catalyst film was first deposited by magnetron sputtering. According to the thickness of the catalytic film, aligned carbon nanotubes were grown with different diameters and spacing, and different length depending the growth time. However, the two major drawbacks are 1) that the location of where the nantoube grows can not be controlled, 2) that the spacing between the nanotubes can not be varied too much. Therefore, we immediately explored to grow aligned carbon nanotubes with the location and spacing controls using e-beam lithography [2]. Unfortunately the cost is so high that the e-beam is not suited for large scale commercialization that requires only an average site density control not the exactly location, for example, electron source. It is the cost issue that made us to develop electrochemical deposition to make catalyst dots that can be separated more than 10 micormeters between dots [3]. With such arrays, we tested many samples for field emission properties and found the optimal site density [4]. However, for applications that require the location controls, for example, photonic band gap crystals, electrochemical deposition can not be satisfactory. It is this kind of application that led us to develop the nanosphere self-assembly technique in large scale [5]. For field emission, we found that ZnO nanowires are good field emitters comparable to carbon nanotubes if they are grown with the right diameter and spacing. Here I will discuss the field emission properties of ZnO nanowires as an alternative material to carbon nanotubes [6]. Us a special kind of carbon nanotubes made by PECVD, we discovered a highly efficient molecular delivery technique, named nanotube spearing, based on the penetration of Ni-particle embedded nanotubes into cell membranes by magnetic field driving. DNA plasmids encoding the enhanced green fluorescent protein (EGFP) sequence were immobilized onto the nanotubes, and subsequently speared into targeted cells. We have achieved the unprecedented high transduction efficiency in Bal17 B-lymphoma, ex vivo B cells, and primary neurons with high viability. This technique may provide a powerful tool for high efficient gene transfer in a variety of cells, especially, the hard-to-transfect cells [7]. Conventional transport studies of multiwall carbon nanotubes (MWNTs) with only the outmost wall contacted to the electrodes via side-contact shows that a MWNT is a ballistic conductor with only the outmost wall carrying current. Here we show, by using end-contact in which every wall is contacted to the electrodes, that every wall is conducting, as evidenced by a significant amount of current drop when an innermost wall is broken at high-bias. Remarkably, the breakdown of each wall was initiated in the middle of the nanotube, not at the contacts, indicating diffusive electron transport. Using end-contact, we were able to probe the conductivity wall-by-wall and found that each wall is indeed either metallic, or semiconducting, or pseudogap-like. These findings not only reveal the intrinsic physical properties of MWNTs but also provide important guidance to MWNT-based electronic devices [8]. At the end of the talk, if time permits, I will talk about our ongoing effort on improving the figure-of-merit (ZT) of thermoelectric materials using a nanocomposite strategy to mimic the structure of the superlattice of PbTe/PbSe and Bi2Te3/Sb2Te3 hoping to reduce the thermal conductivity by a factor of 2–4 while maintaining the electrical conductivity. To make a close to 100% dense nanocomposite, we started with nanoparticles synthesis, then consolidation using both the traditional hot press and the direct current fast-heat, named plasma pressure compact, to preserve the nano size of the component particles. So far, we have seen thermal conductivity decrease by a factor of 2 in the systems of Si/Ge, PbeTe/PbSe, Bi2Te3/Sb2Te3, indicating the potential of improving ZT by a factor of 2.

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Reports on the topic "Genome sequence assembly"

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Schwartz, David C. Microbial genome program report: Optical approaches for physical mapping and sequence assembly of the Deinococcus radiodurans chromosome. Office of Scientific and Technical Information (OSTI), November 1999. http://dx.doi.org/10.2172/758845.

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Faber-Hammond, Joshua, and Kim Brown. Data From: Pseudo-De Novo Assembly and Analysis of Unmapped Genome Sequence Reads in Wild Zebrafish Reveals Novel Gene Content. Portland State University, 2015. http://dx.doi.org/10.15760/data.2.

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Faber-Hammond, Joshua, and Kim Brown. Data From: Anchored Pseudo-De Novo Assembly of Human Genomes Identifies Extensive Sequence Variation from Unmapped Sequence Reads. Portland State University, 2015. http://dx.doi.org/10.15760/data.1.

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