scholarly journals VAPiD: a lightweight cross platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank

2018 ◽  
Author(s):  
Ryan C. Shean ◽  
Negar Makhsous ◽  
Graham D. Stoddard ◽  
Michelle J. Lin ◽  
Alexander L. Greninger
Keyword(s):  
Genome Annotation ◽  
Measles Virus ◽  
Critical Role ◽  
Virus Genome ◽  
Scientific Data ◽  
Human Papillomaviruses ◽  
Command Line ◽  
Annotation Pipeline ◽  
Viral Genomes ◽  
Viral Annotation

AbstractBackgroundWith sequencing technologies becoming cheaper and easier to use, more groups are able to obtain whole genome sequences of viruses of public health and scientific importance. Submission of genomic data to NCBI GenBank is a requirement prior to publication and plays a critical role in making scientific data publicly available.GenBank currently has automatic prokaryotic and eukaryotic genome annotation pipelines but has no viral annotation pipeline beyond influenza virus. Annotation and submission of viral genome sequence is a non-trivial task, especially for groups that do not routinely interact with GenBank for data submissions.ResultsWe present Viral Annotation Pipeline and iDentification (VAPiD), a portable and lightweight command-line tool for annotation and GenBank deposition of viral genomes. VAPiD supports annotation of nearly all unsegmented viral genomes. The pipeline has been validated on human immunodeficiency virus, human parainfluenza virus 1-4, human metapneumovirus, human coronaviruses (229E/OC43/NL63/HKU1/SARS/MERS), human enteroviruses/rhinoviruses, measles virus, mumps virus, Hepatitis A-E Virus, Chikungunya virus, dengue virus, and West Nile virus, as well the human polyomaviruses BK/JC/MCV, human adenoviruses, and human papillomaviruses. The program can handle individual or batch submissions of different viruses to GenBank and correctly annotates multiple viruses, including those that contain ribosomal slippage or RNA editing without prior knowledge of the virus to be annotated. VAPiD is programmed in Python and is compatible with Windows, Linux, and Mac OS systems.ConclusionsWe have created a portable, lightweight, user-friendly, internet-enabled, open-source, command-line genome annotation and submission package to facilitate virus genome submissions to NCBI GenBank. Instructions for downloading and installing VAPiD can be found athttps://github.com/rcs333/VAPiD.

scholarly journals VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Ryan C. Shean ◽  
Negar Makhsous ◽  
Graham D. Stoddard ◽  
Michelle J. Lin ◽  
Alexander L. Greninger
Keyword(s):  
Virus Genome ◽  
Annotation Pipeline ◽  
Cross Platform ◽  
Viral Annotation ◽  
Identification Tool

scholarly journals The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

2015 ◽  
Vol 10 (1) ◽  
Author(s):  
Marcel Huntemann ◽  
Natalia N. Ivanova ◽  
Konstantinos Mavromatis ◽  
H. James Tripp ◽  
David Paez-Espino ◽  
...  
Keyword(s):  
Operating Procedure ◽  
Genome Annotation ◽  
Standard Operating Procedure ◽  
Microbial Genome ◽  
Annotation Pipeline ◽  
Standard Operating

scholarly journals Detection of measles virus genome in bone-marrow aspirates from adults

2002 ◽  
Vol 83 (10) ◽  
pp. 2485-2488 ◽  
Author(s):  
Satomi Sonoda ◽  
Mitsuo Kitahara ◽  
Tetsuo Nakayama
Keyword(s):  
Multiple Myeloma ◽  
Bone Marrow ◽  
Myelodysplastic Syndrome ◽  
Persistent Infection ◽  
Measles Virus ◽  
Adult Population ◽  
Virus Genome ◽  
Malignant Diseases ◽  
Rt Pcr ◽  
Asymptomatic Infections

We investigated the presence of the measles virus genome in order to identify asymptomatic infections in the adult population. Bone-marrow aspirates were obtained from 179 patients, 20–96 years of age, for the diagnosis of malignant diseases (29 with malignant lymphoma, 28 with acute leukaemia, 21 with myelodysplastic syndrome, five with multiple myeloma and 96 with other diseases). The measles virus genome was detected in 17 (9·5%) of 179 individuals by RT–PCR and 28 (15·6%) through hybridization. The genomes detected in bone marrow were all in the same cluster, D5, the strain circulating during the study period, and no evidence of persistent infection was obtained. We conclude that asymptomatic infections of measles virus are common in adults and the presence of the measles virus genome would not be related to the pathogenesis of illness.

Molecular analysis of measles virus genome derived from SSPE and acute measles patients in Papua, New Guinea

2002 ◽  
Vol 68 (1) ◽  
pp. 105-112 ◽  
Author(s):  
Kenji Miki ◽  
Katsuhiro Komase ◽  
Charles S. Mgone ◽  
Ryuta Kawanishi ◽  
Masumi Iijima ◽  
...  
Keyword(s):  
Papua New Guinea ◽  
Molecular Analysis ◽  
Measles Virus ◽  
New Guinea ◽  
Virus Genome

scholarly journals Role of the Undergraduate Student Research Assistant in the New Millennium

2004 ◽  
Vol 3 (4) ◽  
pp. 235-240 ◽  
Author(s):  
Thais Dutra Nascimento Silva ◽  
Lúcia Cristina da Cunha Aguiar ◽  
Jaqueline Leta ◽  
Dilvani Oliveira Santos ◽  
Fernanda Serpa Cardoso ◽  
...  
Keyword(s):  
Undergraduate Students ◽  
Undergraduate Student ◽  
Critical Role ◽  
Academic Research ◽  
Scientific Data ◽  
Research Assistant ◽  
Age Related ◽  
Research Careers ◽  
New Research

In this study, we analyze the contribution of the undergraduate student who participates in the process of generating scientific data and developing a research project using Brazilian research as an example. Historically, undergraduate students have performed the critical role of research assistants in developing countries. This aspect has been underappreciated as a means of generating scientific data in Brazilian research facilities. Brazilian educational institutions are facing major age-related generational changes among the science faculty within the next 5–10 yr. A lack of adequate support for graduate students leads to a concern that undergraduates will not be interested in choosing research assistant programs and, subsequently, academic research careers. To remedy this situation it is important to focus on ways to encourage new research careers and enhance university–industry collaborations.

Applications of Supercomputers in Sequence Analysis and Genome Annotation

2015 ◽  
pp. 149-175
Author(s):  
Gerard G. Dumancas
Keyword(s):  
Sequence Analysis ◽  
High Throughput ◽  
Genome Annotation ◽  
Critical Role ◽  
Time Saving ◽  
Genetic Causes ◽  
Modern Era

In the modern era of science, bioinformatics play a critical role in unraveling the potential genetic causes of various diseases. Two of the most important areas of bioinformatics today, sequence analysis and genome annotation, are essential for the success of identifying the genes responsible for different diseases. These two emerging areas utilize highly intensive mathematical calculations in order to carry out the processes. Supercomputers facilitate such calculations in an efficient and time-saving manner generating high-throughput images. Thus, this chapter thoroughly discusses the applications of supercomputers in the areas of sequence analysis and genome annotation. This chapter also showcases sophisticated software and algorithms utilized by the two mentioned areas of bioinformatics.

scholarly journals Viral invasion fitness across a continuum from lysis to latency†

2019 ◽  
Vol 5 (1) ◽  
Author(s):  
Joshua S Weitz ◽  
Guanlin Li ◽  
Hayriye Gulbudak ◽  
Michael H Cortez ◽  
Rachel J Whitaker
Keyword(s):  
High Growth ◽  
Theoretical Framework ◽  
Virus Genome ◽  
Environmental Drivers ◽  
Natural Environments ◽  
Chronic Infections ◽  
Viral Genomes ◽  
Virus Particles ◽  
Invasion Fitness ◽  
Prevailing Paradigm

Abstract The prevailing paradigm in ecological studies of viruses and their microbial hosts is that the reproductive success of viruses depends on the proliferation of the ‘predator’, that is, the virus particle. Yet, viruses are obligate intracellular parasites, and the virus genome—the actual unit of selection—can persist and proliferate from one cell generation to the next without lysis or the production of new virus particles. Here, we propose a theoretical framework to quantify the invasion fitness of viruses using an epidemiological cell-centric metric that focuses on the proliferation of viral genomes inside cells instead of virus particles outside cells. This cell-centric metric enables direct comparison of viral strategies characterized by obligate killing of hosts (e.g. via lysis), persistence of viral genomes inside hosts (e.g. via lysogeny), and strategies along a continuum between these extremes (e.g. via chronic infections). As a result, we can identify environmental drivers, life history traits, and key feedbacks that govern variation in viral propagation in nonlinear population models. For example, we identify threshold conditions given relatively low densities of susceptible cells and relatively high growth rates of infected cells in which lysogenic and other chronic strategies have higher potential viral reproduction than lytic strategies. Altogether, the theoretical framework helps unify the ongoing study of eco-evolutionary drivers of viral strategies in natural environments.

Measles Virus Genome in Infections of the Central Nervous System

1981 ◽  
Vol 144 (2) ◽  
pp. 154-160 ◽  
Author(s):  
A. T. Haase ◽  
P. Swoveland ◽  
L. Stowring ◽  
P. Ventura ◽  
K. P. Johnson ◽  
...  
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Measles Virus ◽  
Virus Genome ◽  
The Central Nervous System

scholarly journals In Vitro and In Vivo Biology of Recombinant Adenovirus Vectors with E1, E1/E2A, or E1/E4 Deleted

1998 ◽  
Vol 72 (3) ◽  
pp. 2022-2032 ◽  
Author(s):  
M. Lusky ◽  
M. Christ ◽  
K. Rittner ◽  
A. Dieterle ◽  
D. Dreyer ◽  
...  
Keyword(s):  
Recombinant Adenovirus ◽  
Virus Genome ◽  
Minor Role ◽  
Immunodeficient Mice ◽  
Viral Genomes ◽  
Viral Genes ◽  
Adenovirus Vectors ◽  
A Minor

ABSTRACT Isogenic, E3-deleted adenovirus vectors defective in E1, E1 and E2A, or E1 and E4 were generated in complementation cell lines expressing E1, E1 and E2A, or E1 and E4 and characterized in vitro and in vivo. In the absence of complementation, deletion of both E1 and E2A completely abolished expression of early and late viral genes, while deletion of E1 and E4 impaired expression of viral genes, although at a lower level than the E1/E2A deletion. The in vivo persistence of these three types of vectors was monitored in selected strains of mice with viral genomes devoid of transgenes to exclude any interference by immunogenic transgene-encoded products. Our studies showed no significant differences among the vectors in the short-term maintenance and long-term (4-month) persistence of viral DNA in liver and lung cells of immunocompetent and immunodeficient mice. Furthermore, all vectors induced similar antibody responses and comparable levels of adenovirus-specific cytotoxic T lymphocytes. These results suggest that in the absence of transgenes, the progressive deletion of the adenovirus genome does not extend the in vivo persistence of the transduced cells and does not reduce the antivirus immune response. In addition, our data confirm that, in the absence of transgene expression, mouse cellular immunity to viral antigens plays a minor role in the progressive elimination of the virus genome.

scholarly journals Insights into the Selective Pressures Restricting Pelargonium Flower Break Virus Genome Variability: Evidence for Host Adaptation

2006 ◽  
Vol 80 (16) ◽  
pp. 8124-8132 ◽  
Author(s):  
Patricia Rico ◽  
Pilar Ivars ◽  
Santiago F. Elena ◽  
Carmen Hernández
Keyword(s):  
Amino Acid ◽  
Leucine Zipper ◽  
Critical Role ◽  
Chenopodium Quinoa ◽  
Virus Genome ◽  
Acid Sites ◽  
Genomic Region ◽  
Amino Acid Sequences ◽  
Nucleotide Substitutions ◽  
Selective Pressures

ABSTRACT The molecular diversity of Pelargonium flower break virus (PFBV) was assessed using a collection of isolates from different geographical origins, hosts, and collecting times. The genomic region examined was 1,828 nucleotides (nt) long and comprised the coding sequences for the movement (p7 and p12) and the coat (CP) proteins, as well as flanking segments including the entire 3′ untranslated region (3′ UTR). Some constraints limiting viral heterogeneity could be inferred from sequence analyses, such as the conservation of the amino acid sequences of p7 and of the shell domain of the CP, the maintenance of a leucine zipper motif in p12, and the preservation of a particular folding in the 3′ UTR. A remarkable covariation, involving five specific amino acid sites, was found in the CP of isolates largely propagated in the local lesion host Chenopodium quinoa and in the progeny of a PFBV variant subjected to serial passages in this host. Concomitant with this covariation, up to 30 nucleotide substitutions in a 1,428-nt region of the viral RNA could be attributable to C. quinoa-specific adaptation, representing one of the most outstanding cases of host-driven genome variation for a plant virus. Globally, the results indicate that the selective pressures exerted by the host play a critical role in shaping PFBV populations and that these populations are likely being selected for at both protein and RNA levels.

Sign in / Sign up

Export Citation Format

Share Document