scholarly journals The Genome of Salmonid Herpesvirus 1

1998 ◽  
Vol 72 (3) ◽  
pp. 1974-1982 ◽  
Author(s):  
Andrew J. Davison
Keyword(s):  
Dna Hybridization ◽  
Large Scale ◽  
Sequence Data ◽  
Complete Sequence ◽  
Unique Region ◽  
Channel Catfish Virus ◽  
Dna Sequence Data ◽  
Herpesvirus 1 ◽  
Endonuclease Mapping ◽  
Single Orientation

ABSTRACT Salmonid herpesvirus 1 (SalHV-1) is a pathogen of the rainbow trout (Oncorhynchus mykiss). Restriction endonuclease mapping, cosmid cloning, DNA hybridization, and targeted DNA sequencing experiments showed that the genome is 174.4 kbp in size, consisting of a long unique region (UL; 133.4 kbp) linked to a short unique region (US; 25.6 kbp) which is flanked by an inverted repeat (RS; 7.7 kbp). US is present in virion DNA in either orientation, but UL is present in a single orientation. This structure is characteristic of theVaricellovirus genus of the subfamilyAlphaherpesvirinae but has evidently evolved independently, since an analysis of randomly sampled DNA sequence data showed that SalHV-1 shares at least 18 genes with channel catfish virus (CCV), a fish herpesvirus whose complete sequence is known and which is unrelated to mammalian herpesviruses. The use of oligonucleotide probes demonstrated that in comparison with CCV, the conserved SalHV-1 genes are located in UL in at least five rearranged blocks. Large-scale gene rearrangements of this type are also characteristic of the three mammalian herpesvirus subfamilies. The junction between two SalHV-1 gene blocks was confirmed by sequencing a 4,245-bp region which contains the dUTPase gene, part of a putative spliced DNA polymerase gene, and one other complete gene. The implications of these findings in herpesvirus taxonomy are discussed.

scholarly journals Self-organizing Clustering: Non-hierarchical Clustering for Large Scale DNA Sequence Data

2007 ◽  
Vol 3 ◽  
pp. 193-197 ◽  
Author(s):  
Kou Amano ◽  
Hiroaki Ichikawa ◽  
Hidemitsu Nakamura ◽  
Hisataka Numa ◽  
Kaoru Fukami-Kobayashi ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Hierarchical Clustering ◽  
Large Scale ◽  
Sequence Data ◽  
Dna Sequence Data ◽  
Self Organizing

scholarly journals Sequence variation aware genome references and read mapping with the variation graph toolkit

2017 ◽  
Author(s):  
Erik Garrison ◽  
Jouni Sirén ◽  
Adam M. Novak ◽  
Glenn Hickey ◽  
Jordan M. Eizenga ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Large Scale ◽  
De Novo ◽  
Sequence Data ◽  
Variant Calling ◽  
Read Mapping ◽  
Dna Sequence Data ◽  
Suffix Arrays ◽  
Improved Accuracy ◽  
Reference Genomes

AbstractReference genomes guide our interpretation of DNA sequence data. However, conventional linear references are fundamentally limited in that they represent only one version of each locus, whereas the population may contain multiple variants. When the reference represents an individual’s genome poorly, it can impact read mapping and introduce bias. Variation graphs are bidirected DNA sequence graphs that compactly represent genetic variation, including large scale structural variation such as inversions and duplications.1 Equivalent structures are produced by de novo genome assemblers.2,3 Here we present vg, a toolkit of computational methods for creating, manipulating, and utilizing these structures as references at the scale of the human genome. vg provides an efficient approach to mapping reads onto arbitrary variation graphs using generalized compressed suffix arrays,4 with improved accuracy over alignment to a linear reference, creating data structures to support downstream variant calling and genotyping. These capabilities make using variation graphs as reference structures for DNA sequencing practical at the scale of vertebrate genomes, or at the topological complexity of new species assemblies.

scholarly journals NEW MOLECULAR MARKERS IN Hydrangea AND THEIR USEFULLNESS IN EVALUATING DIVERSITY, VERIFYING HYBRIDS, AND UNCOVERING GENES

HortScience ◽  
2005 ◽  
Vol 40 (3) ◽  
pp. 881b-881
Author(s):  
Tim Rinehart ◽  
Sandy Reed
Keyword(s):  
Species Diversity ◽  
Large Scale ◽  
Sequence Data ◽  
Issr Markers ◽  
Future Research ◽  
Species Variation ◽  
Marker Assisted Breeding ◽  
Dna Sequence Data ◽  
Hydrangea Macrophylla ◽  
Limited Usefulness

Hydrangea popularity and use in the landscape has expanded rapidly in recent years with the addition of remontant varieties. Most cultivars in production belong to the species Hydrangea macrophylla but H. paniculata, H. arborescens, H. serrata, H. aspera, H. heteromalla, H. integrifolia, H. anomala, H. seemanii, and H. quercifolia are also commercially available. In addition to species diversity there is high intra-species variation, particularly in H. macrophylla, which includes mopheads, lacecaps, French, Japanese, dwarf, and variegated varieties. Relatively little is known about the genetic background or combinability of these plants. DNA sequence data, genome size, RAPD, AFLP, and ISSR markers have been used for taxonomic identification and to estimate diversity within the genus. All of these methods have limited usefulness in a large scale breeding program. We recently established microsatellite markers for Hydrangea and evaluated their utility for estimating species diversity and identifying cultivars within H. macrophylla and H. paniculata. We also verified an inter-specific cross between H. macrophylla and H. paniculata using these markers. Future research includes marker assisted breeding, particularly with respect to remontant flowering traits.

scholarly journals annonex2embl: automatic preparation of annotated DNA sequences for bulk submissions to ENA

2020 ◽  
Vol 36 (12) ◽  
pp. 3841-3848
Author(s):  
Michael Gruenstaeudl
Keyword(s):  
Dna Sequences ◽  
Large Scale ◽  
Sequence Data ◽  
Complete Sequence ◽  
Supplementary Information ◽  
Biological Research ◽  
Sequence Alignments ◽  
Easy Integration ◽  
Central Pillar ◽  
Python Package

Abstract Motivation The submission of annotated sequence data to public sequence databases constitutes a central pillar in biological research. The surge of novel DNA sequences awaiting database submission due to the application of next-generation sequencing has increased the need for software tools that facilitate bulk submissions. This need has yet to be met with the concurrent development of tools to automate the preparatory work preceding such submissions. Results The author introduce annonex2embl, a Python package that automates the preparation of complete sequence flatfiles for large-scale sequence submissions to the European Nucleotide Archive. The tool enables the conversion of DNA sequence alignments that are co-supplied with sequence annotations and metadata to submission-ready flatfiles. Among other features, the software automatically accounts for length differences among the input sequences while maintaining correct annotations, automatically interlaces metadata to each record and displays a design suitable for easy integration into bioinformatic workflows. As proof of its utility, annonex2embl is employed in preparing a dataset of more than 1500 fungal DNA sequences for database submission. Availability and implementation annonex2embl is freely available via the Python package index at http://pypi.python.org/pypi/annonex2embl. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals A Show of Character—a further response to Wiley et al.

Zootaxa ◽  
2011 ◽  
Vol 2946 (1) ◽  
pp. 29 ◽  
Author(s):  
ANTHONY C. GILL ◽  
RANDALL D. MOOI
Keyword(s):  
Dna Sequence ◽  
Large Scale ◽  
Sequence Data ◽  
Molecular Data ◽  
Scientific Rigor ◽  
Dna Sequence Data ◽  
Phylogenetic Hypotheses ◽  
Alternative Relationships

Wiley et al. (2011) begin their critique of our paper (Mooi & Gill, 2010) with an assertion: “we need to make itclear that the foundation of their arguments rests not on scientific rigor, but rather on opinions about the re-classification of fishes using molecular data. This bias is the reason that they only targeted researchers who proposed changes in the higher-level taxonomy of fishes using phylogenetic hypotheses based on DNA sequence data (Miya et al. 2007, Smith & Craig 2007, Thacker 2009). In criticizing these studies, they do not suggest any alternative relationships or provide any counter evidence to the proposed relationships.” And on page 8, they apparently read our thoughts (aside from the title, none of the words in quotations was written by us in that context) and concluded: “Mooi & Gill entitled their paper “A crisis in fish systematics” because they long for the days when “real” ichthyologists found “meaningful” characters and “true” relationships.” Finally (p. 9), they contend that “Mooi & Gill’s various studies are usually focused on Johnson & Patterson’s (1993: 555) “disparate twigs of the [percomorph] tree,” whereas the explicit studies they criticize are large-scale and taxon rich datasets that have not otherwise been analyzed in Percomorpha.”

scholarly journals Data Attribution from Download to Publication

2018 ◽  
Vol 2 ◽  
pp. e26060
Author(s):  
Pamela Soltis
Keyword(s):  
Natural History ◽  
Large Scale ◽  
Sequence Data ◽  
Research Process ◽  
Global Biodiversity Information Facility ◽  
Data Set ◽  
Dna Sequence Data ◽  
Large Scale Data ◽  
Data Tracking ◽  
Biodiversity Information

Digitized natural history data are enabling a broad range of innovative studies of biodiversity. Large-scale data aggregators such as Global Biodiversity Information facility (GBIF) and Integrated Digitized Biocollections (iDigBio) provide easy, global access to millions of specimen records contributed by thousands of collections. A developing community of eager users of specimen data – whether locality, image, trait, etc. – is perhaps unaware of the effort and resources required to curate specimens, digitize information, capture images, mobilize records, serve the data, and maintain the infrastructure (human and cyber) to support all of these activities. Tracking of specimen information throughout the research process is needed to provide appropriate attribution to the institutions and staff that have supplied and served the records. Such tracking may also allow for annotation and comment on particular records or collections by the global community. Detailed data tracking is also required for open, reproducible science. Despite growing recognition of the value and need for thorough data tracking, both technical and sociological challenges continue to impede progress. In this talk, I will present a brief vision of how application of a DOI to each iteration of a data set in a typical research project could provide attribution to the provider, opportunity for comment and annotation of records, and the foundation for reproducible science based on natural history specimen records. Sociological change – such as journal requirements for data deposition of all iterations of a data set – can be accomplished using community meetings and workshops, along with editorial efforts, as were applied to DNA sequence data two decades ago.

scholarly journals annonex2embl: automatic preparation of annotated DNA sequences for bulk submissions to ENA

2019 ◽  
Author(s):  
Michael Gruenstaeudl
Keyword(s):  
Dna Sequences ◽  
Large Scale ◽  
Sequence Data ◽  
Complete Sequence ◽  
Biological Research ◽  
Sequence Alignments ◽  
European Nucleotide Archive ◽  
Concurrent Development ◽  
Easy Integration ◽  
Central Pillar

ABSTRACTMotivationThe submission of annotated sequence data to public sequence databases constitutes a central pillar in biological research. The surge of novel DNA sequences awaiting database submission due to the application of next-generation sequencing has increased the need for software tools that facilitate bulk submissions. This need has yet to be met with a concurrent development of tools to automate the preparatory work preceding such submissions.ResultsI introduce annonex2embl, a Python package that automates the preparation of complete sequence flatfiles for large-scale sequence submissions to the European Nucleotide Archive. The tool enables the conversion of DNA sequence alignments that are co-supplied with sequence annotations and metadata to submission-ready flatfiles. Among other features, the software automatically accounts for length differences among the input sequences while maintaining correct annotations, automatically interlaces metadata to each record, and displays a design suitable for easy integration into bioinformatic workflows. As proof of its utility, annonex2embl is employed in preparing a dataset of more than 1,500 fungal DNA sequences for database submission.

scholarly journals Temporal lags and overlap in the diversification of weevils and flowering plants

2009 ◽  
Vol 106 (17) ◽  
pp. 7083-7088 ◽  
Author(s):  
Duane D. McKenna ◽  
Andrea S. Sequeira ◽  
Adriana E. Marvaldi ◽  
Brian D. Farrell
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Divergence Times ◽  
Resource Tracking ◽  
Crown Group ◽  
Dna Sequence Data ◽  
Angiosperm Diversification ◽  
History Of ◽  
Fossil Data ◽  
Diversification Event

The extraordinary diversity of herbivorous beetles is usually attributed to coevolution with angiosperms. However, the degree and nature of contemporaneity in beetle and angiosperm diversification remain unclear. Here we present a large-scale molecular phylogeny for weevils (herbivorous beetles in the superfamily Curculionoidea), one of the most diverse lineages of insects, based on ≈8 kilobases of DNA sequence data from a worldwide sample including all families and subfamilies. Estimated divergence times derived from the combined molecular and fossil data indicate diversification into most families occurred on gymnosperms in the Jurassic, beginning ≈166 Ma. Subsequent colonization of early crown-group angiosperms occurred during the Early Cretaceous, but this alone evidently did not lead to an immediate and major diversification event in weevils. Comparative trends in weevil diversification and angiosperm dominance reveal that massive diversification began in the mid-Cretaceous (ca.112.0 to 93.5 Ma), when angiosperms first rose to widespread floristic dominance. These and other evidence suggest a deep and complex history of coevolution between weevils and angiosperms, including codiversification, resource tracking, and sequential evolution.

scholarly journals Dynamic Planning of Bicycle Stations in Dockless Public Bicycle-sharing System Using Gated Graph Neural Network

2021 ◽  
Vol 12 (2) ◽  
pp. 1-22
Author(s):  
Jianguo Chen ◽  
Kenli Li ◽  
Keqin Li ◽  
Philip S. Yu ◽  
Zeng Zeng
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Location Prediction ◽  
City Management ◽  
Dynamic Planning ◽  
Graph Sequence ◽  
Graph Modeling ◽  
The Government ◽  
Location Clustering ◽  
Station Location

Benefiting from convenient cycling and flexible parking locations, the Dockless Public Bicycle-sharing (DL-PBS) network becomes increasingly popular in many countries. However, redundant and low-utility stations waste public urban space and maintenance costs of DL-PBS vendors. In this article, we propose a Bicycle Station Dynamic Planning (BSDP) system to dynamically provide the optimal bicycle station layout for the DL-PBS network. The BSDP system contains four modules: bicycle drop-off location clustering, bicycle-station graph modeling, bicycle-station location prediction, and bicycle-station layout recommendation. In the bicycle drop-off location clustering module, candidate bicycle stations are clustered from each spatio-temporal subset of the large-scale cycling trajectory records. In the bicycle-station graph modeling module, a weighted digraph model is built based on the clustering results and inferior stations with low station revenue and utility are filtered. Then, graph models across time periods are combined to create a graph sequence model. In the bicycle-station location prediction module, the GGNN model is used to train the graph sequence data and dynamically predict bicycle stations in the next period. In the bicycle-station layout recommendation module, the predicted bicycle stations are fine-tuned according to the government urban management plan, which ensures that the recommended station layout is conducive to city management, vendor revenue, and user convenience. Experiments on actual DL-PBS networks verify the effectiveness, accuracy, and feasibility of the proposed BSDP system.

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