Viruses and Bioinformatics from Virology.uvic.ca
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PhiSiGns

PhiSiGns | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

PhiSiGns is a web-based and standalone application that provides a simple and convenient tool to identify signature genes and design primers for PCR amplification of related genes from environmental samples.

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Viruses and Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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It's a group effort - the curators:

It's a group effort - the curators: | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

get in touch if you want to help curate this topic

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Bwana Moses's comment, May 25, 2016 6:13 AM
Great work. Keep it going.
Bwana Moses's comment, March 7, 12:46 PM
Thank You.
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Highly efficient maternal-fetal Zika virus transmission in pregnant rhesus macaques

Highly efficient maternal-fetal Zika virus transmission in pregnant rhesus macaques | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Maternal ZIKV infection in pregnancy is associated with severe fetal anomalies, including microcephaly. It has been shown that infection manifests differently in pregnancy than in the non-pregnant state, with prolonged maternal viremia. ZIKV is spread by mosquitos and through sexual contact and since its first detection in early 2015, has become endemic to the Americas. While much has been learned from studying infected human pregnancies, there are still many questions concerning transmission of ZIKV from mother to fetus. Investigating ZIKV infection in non-human primates could help answer these questions due to similarities in the immune system, and the tissues separating the fetus from the mother during pregnancy. Our study serves to model ZIKV transmission in early and late pregnancy, as well as study the effects of this infection on the fetus and mother at these different times in pregnancy. The data collected provides an important insight on ZIKV in pregnancy where the pregnancies have been monitored throughout the entire infection period until term, and suggests that vertical transmission may be very efficient, although severe fetal outcomes are uncommon.

Via Ed Rybicki
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DNA-Binding Properties of African Swine Fever Virus pA104R, a Histone-Like Protein Involved in Viral Replication and Transcription

MPORTANCE Recently reintroduced in Europe, African swine fever virus (ASFV) causes a fatal disease in domestic pigs, causing high economic losses in affected countries, as no vaccine or treatment is currently available. Remarkably, ASFV is the only known mammalian virus that putatively codes for a histone-like protein (pA104R) that shares extensive sequence homology with bacterial histone-like proteins. In this study, we characterized the DNA-binding properties of pA104R, analyzed the functional importance of two conserved residues, and showed that pA104R and ASFV topoisomerase II cooperate and display DNA-supercoiling activity. Moreover, pA104R is expressed during the late phase of infection and accumulates in viral DNA replication sites, and its downregulation revealed that pA104R is required for viral DNA replication and transcription. These results suggest that pA104R participates in the modulation of viral DNA topology and genome packaging, indicating that A104R deletion mutants may be a good strategy for vaccine development against ASFV.
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Encephalitis associated with human herpesvirus-7 infection in an immunocompetent adult

Encephalitis associated with human herpesvirus-7 infection in an immunocompetent adult | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Primary Human herpesvirus-7 (HHV-7) infection usually occurs during childhood and causes several clinical manifestations: mainly exanthem subitum (roseola infantum), followed by a lifelong latent state with possible reactivation in case of immunodeficiency. Nevertheless, some considerably different approaches exist regarding the natural history of HHV-7 and the possible consequences of HHV-7 infection in immunocompetent adults. In particular, little is known about its pathogenic role in central nervous system (CNS) disease in nonimmunosuppressed adults. Specifically, in case of encephalitis, it is important to distinguish between infectious encephalitis and postinfectious encephalomyelitis for the management of patients We describe here a case of encephalitis associated to human herpesvirus-7 with associated polymyeloradiculopathy in an immunocompetent patient which may contribute to the delineation of the approach to a patient profile with a similar clinical presentation and evolution to those presented in the literature. This case may alert clinicians to consider this specific etiology in the differential diagnosis of encephalopathy in patients with suspected infectious encephalitis who do not respond to acyclovir or in patients who develop acute polymyeloradiculopathy, considering that HHV-7 may be a pathological factor and that a timely diagnosis is crucial for the early administration of specific treatment.
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515 Free Online Programming & Computer Science Courses You Can Start Now

515 Free Online Programming & Computer Science Courses You Can Start Now | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Five years ago, universities like MIT and Stanford first opened up free online courses to the public. Today, more than 700 schools around the world have created thousands of free online courses.


Via Dr. Stefan Gruenwald
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The link between adjacent codon pairs and mRNA stability

The link between adjacent codon pairs and mRNA stability | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Evidence in diverse organisms suggests that codon optimality is a major determinant of mRNA translation and degradation. Codon optimality is thought to act by modulating the efficiency of ribosome elongation. In Saccharomyces cerevisiae, a recent study has identified 17 adjacent codon pairs that mediate strong inhibition of translation elongation. However, relationships between the inhibitory codon pairs and other aspects of gene expression are unknown. To gain insights into how the inhibitory codon pairs may affect aspects of gene expression, we utilized existing datasets to conduct genome-scale analyses in S. cerevisiae. Our analysis revealed the following points. First, the inhibitory codon pairs are significantly associated with faster mRNA decay. The association is not solely due to the content of nucleotides, individual codons, or dipeptides encoded by the inhibitory codon pairs. Second, the inhibitory codon pairs cannot fully explain the previously known relationship of codon optimality with mRNA stability, suggesting that optimality of individual codons and properties of adjacent codon pairs both contribute to gene regulation. Finally, although the inhibitory codon pairs are associated with slower mRNA synthesis and protein instability, the associations can be attributed to usage bias in individual codons. This study suggests an association of inhibitory codon pairs with mRNA stability and thus another layer of complexity in the codon-mediated gene regulation.
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A scalable and memory-efficient algorithm for de novo transcriptome assembly of non-model organisms

A scalable and memory-efficient algorithm for de novo transcriptome assembly of non-model organisms | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
With increased availability of de novo assembly algorithms, it is feasible to study entire transcriptomes of non-model organisms. While algorithms are available that are specifically designed for performing transcriptome assembly from high-throughput sequencing data, they are very memory-intensive, limiting their applications to small data sets with few libraries. We develop a transcriptome assembly algorithm that recovers alternatively spliced isoforms and expression levels while utilizing as many RNA-Seq libraries as possible that contain hundreds of gigabases of data. New techniques are developed so that computations can be performed on a computing cluster with moderate amount of physical memory. Our strategy minimizes memory consumption while simultaneously obtaining comparable or improved accuracy over existing algorithms. It provides support for incremental updates of assemblies when new libraries become available.
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Immune Tolerant Chronic Hepatitis B: The Unrecognized Risks

Immune Tolerant Chronic Hepatitis B: The Unrecognized Risks | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Chronic infection with hepatitis B virus (HBV) progresses through multiple phases, including immune tolerant, immune active, immune control, and, in a subset of patients who achieve immune control, reactivation. The first, the immune tolerant phase, is considered to be prolonged in duration but essentially benign in nature, lacking long-term consequences, and thus not recommended for antiviral therapy. This review challenges the notion that the immune tolerant phase is truly benign and considers the possibility that events during this phase may contribute significantly to cirrhosis, hepatocellular carcinoma (HCC), and the premature death of 25% of HBV carriers worldwide. Thus, earlier treatment than recommended by current guidelines should be considered. Low therapeutic coverage exacerbated by restrictive treatment guidelines may facilitate disease progression in many patients but also increase the risk of neonatal and horizontal transmission from untreated mothers to their children. While a prophylactic vaccine exists, there are many areas worldwide where the treatment of adults and the delivery of an effective vaccination course to newborns present difficult challenges.
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Bacterial Virus Ontology; Coordinating across Databases

Bacterial viruses, also called bacteriophages, display a great genetic diversity and utilize unique processes for infecting and reproducing within a host cell. All these processes were investigated and indexed in the ViralZone knowledge base. To facilitate standardizing data, a simple ontology of viral life-cycle terms was developed to provide a common vocabulary for annotating data sets. New terminology was developed to address unique viral replication cycle processes, and existing terminology was modified and adapted. Classically, the viral life-cycle is described by schematic pictures. Using this ontology, it can be represented by a combination of successive events: entry, latency, transcription/replication, host–virus interactions and virus release. Each of these parts is broken down into discrete steps. For example enterobacteria phage lambda entry is broken down in: viral attachment to host adhesion receptor, viral attachment to host entry receptor, viral genome ejection and viral genome circularization. To demonstrate the utility of a standard ontology for virus biology, this work was completed by annotating virus data in the ViralZone, UniProtKB and Gene Ontology databases.
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A multi-purpose toolkit to enable advanced genome engineering in plants - Plant Cell

A multi-purpose toolkit to enable advanced genome engineering in plants - Plant Cell | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Cermak et al, 2017

We report a comprehensive toolkit that enables targeted, specific modification of monocot and dicot genomes using a variety of genome engineering approaches. Our reagents, based on TALENs and the CRISPR/Cas9 system, are systematized for fast, modular cloning and accommodate diverse regulatory sequences to drive reagent expression. Vectors are optimized to create either single or multiple gene knockouts and large chromosomal deletions. Moreover, integration of geminivirus-based vectors enables precise gene editing through homologous recombination. Regulation of transcription is also possible. A web-based tool greatly streamlines vector selection and construction. One advantage of our platform is the use of the Csy4 ribonuclease and tRNA processing enzymes to simultaneously express multiple guide RNAs (gRNAs). For example, we demonstrate targeted deletions in up to six genes by expressing twelve gRNAs from a single transcript. Csy4 and tRNA expression systems are almost twice as effective in inducing mutations as gRNAs expressed from individual RNA polymerase III (Pol III) promoters. Mutagenesis can be further enhanced 2.5-fold by incorporating the TREX2 exonuclease. Finally, we demonstrate that Cas9 nickases induce gene targeting at frequencies comparable to native Cas9 when they are delivered on geminivirus replicons. The reagents have been successfully validated in tomato, tobacco, Medicago, wheat and barley.


Via dromius
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Editorial overview: Viral immunology: Dealing with bad news

Understanding immunity to viruses therefore encompasses many, if not nearly all aspects of cell biology and immunology. A positive trend of the past twenty years of viral research is that the connection between viruses and innate cellular anti-viral mechanisms has cemented virology as an important sub-discipline of cell biology, and converted many virologists into at least honorary immunologists. The inherent simplicity of viruses and their marked tendency towards robust expression of their proteome and flagrant manipulation of host cells and immunity, make them superb tools to make basic discoveries.

Pragmatically, basic research in viral immunology provides the foundation for improving and developing new anti-viral vaccines and therapies. Recent outbreaks of MERs, Ebola and Zika viruses provide a pointed reminder of the threat that rapidly evolving viruses pose to human health and even existence, and underscore the importance of having a sufficient understanding of virus host interactions to quickly develop vaccines.

This issue of Current Opinion in Virology features eight outstanding reviews that summarize current knowledge of a number of the immune hurdles to viral replication. The immune system can be broadly, if imprecisely divided into innate vs. adaptive elements. Innate immunity is generally immediate and agent non-specific. Adaptive immunity is based on the functions of B and T cells, which due to their high antigen specificity, exist in relatively small numbers at the start of infection of a naïve host, and need nearly a week of exceedingly rapid division to attain fighting strength (four to six doublings per day, for six days geometrically increases their numbers up to 16 million-fold).
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MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud | Bioinformatics | Oxford Academic

Summary: This paper presents MarDRe, a de novo cloud-ready duplicate and near-duplicate removal tool that can process single-end and paired-end reads from FASTQ/FASTA datasets. MarDRe takes advantage of the widely adopted MapReduce programming model to fully exploit Big Data technologies on cloud-based infrastructures. Written in Java to maximize cross-platform compatibility, MarDRe is built upon the open-source Apache Hadoop project, the most popular distributed computing framework for scalable Big Data processing. On a 16-node cluster deployed on the Amazon EC2 cloud platform, MarDRe is up to 8.52 times faster than a representative state-of-the-art tool.
Availability and Implementation: Source code in Java and Hadoop as well as a user’s guide are freely available under the GNU GPLv3 license at http://mardre.des.udc.es.
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Ahead of Print -Novel Retinal Lesion in Ebola Survivors, Sierra Leone,  - CDC

We conducted a case–control study in Freetown, Sierra Leone, to investigate ocular signs in Ebola virus disease (EVD) survivors. A total of 82 EVD survivors with ocular symptoms and 105 controls from asymptomatic civilian and military personnel and symptomatic eye clinic attendees underwent ophthalmic examination, including widefield retinal imaging. Snellen visual acuity was <6/7.5 in 75.6% (97.5% CI 63%–85.7%) of EVD survivors and 75.5% (97.5% CI 59.1%–87.9%) of controls. Unilateral white cataracts were present in 7.4% (97.5% CI 2.4%–16.7%) of EVD survivors and no controls. Aqueous humor from 2 EVD survivors with cataract but no anterior chamber inflammation were PCR-negative for Zaire Ebola virus, permitting cataract surgery. A novel retinal lesion following the anatomic distribution of the optic nerve axons occurred in 14.6% (97.5% CI 7.1%–25.6%) of EVD survivors and no controls, suggesting neuronal transmission as a route of ocular entry.
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Research team develops test to detect hidden HIV

Research team develops test to detect hidden HIV | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The quest to develop a cure for HIV has long been plagued by a seemingly simple question: How do doctors determine if someone is cured? The virus has a knack for lying dormant in immune cells at levels undetectable to al
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Sorting out HIV

Researchers at EMBL, ESPCI Paris, and the International AIDS Vaccine Initiative have developed a new technique for rapidly sorting HIV viruses, which could lead to more rapid development o
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New releases from NCBI: IgBLAST 1.7.0 and Sequence Viewer 3.21

New releases from NCBI: IgBLAST 1.7.0 and Sequence Viewer 3.21 | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
IgBLAST 1.7.0 release

A new version of IgBLAST is now available on FTP, with the following new features:

Specify whether overlapping nucleotides at VDJ junctions are allowed in matching V, D, and J genes.
Set a custom J gene mismatch penalty
Report the CDR3 start and stop positions in the sub-region table
Use alignment length instead of percent identity as the tie-breaker for hits with identical blast scores, improving accuracy in the V, D, J gene assignment.
IgBLAST was developed at the NCBI to facilitate the analysis of immunoglobulin and T cell receptor variable domain sequences.
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Staying Current in Bioinformatics & Genomics: 2017 Edition

Staying Current in Bioinformatics & Genomics: 2017 Edition | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Stephen Turner is an assistant professor of public health sciences and director of the Bioinformatics Core at the University of Virginia.

 

It has taken Stephen almost a decade to compile and continually hone this list of resources to the things that are useful and relevant. This is what works for him, now, in 2017. It’s not a one-size-fits-all list, and 2018 will probably have a somewhat different list, but Stephen hopes you’ll find the current list useful.


Via Dr. Stefan Gruenwald
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Phylogenetic trees in R using ggtree

Phylogenetic trees in R using ggtree | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Recently, one R package which I like to use for visualizing phylogenetic trees got published. It’s called ggtree, and as you might guess from the name it is based on the popular ggplot2 packa…
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Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples

Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Next generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools capable of parallel processing of virome sequencing data by exactly identical methods: this is especially important in studies of multifactorial diseases, or in parallel comparison of laboratory protocols. We have developed a web-based application allowing direct upload of sequences from multiple virome samples using custom parameters. The samples are then processed in parallel using an identical protocol, and can be easily reanalyzed. The pipeline performs de-novo assembly, taxonomic classification of viruses as well as sample analyses based on user-defined grouping categories. Tables of virus abundance are produced from cross-validation by remapping the sequencing reads to a union of all observed reference viruses. In addition, read sets and reports are created after processing unmapped reads against known human and bacterial ribosome references. Secured interactive results are dynamically plotted with population and diversity charts, clustered heatmaps and a sortable and searchable abundance table. The Vipie web application is a unique tool for multi-sample metagenomic analysis of viral data, producing searchable hits tables, interactive population maps, alpha diversity measures and clustered heatmaps that are grouped in applicable custom sample categories. Known references such as human genome and bacterial ribosomal genes are optionally removed from unmapped (‘dark matter’) reads. Secured results are accessible and shareable on modern browsers. Vipie is a freely available web-based tool whose code is open source.
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Distinct Contributions of Autophagy Receptors in Measles Virus Replication

Distinct Contributions of Autophagy Receptors in Measles Virus Replication | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Autophagy is a potent cell autonomous defense mechanism that engages the lysosomal pathway to fight intracellular pathogens. Several autophagy receptors can recognize invading pathogens in order to target them towards autophagy for their degradation after the fusion of pathogen-containing autophagosomes with lysosomes. However, numerous intracellular pathogens can avoid or exploit autophagy, among which is measles virus (MeV). This virus induces a complete autophagy flux, which is required to improve viral replication. We therefore asked how measles virus interferes with autophagy receptors during the course of infection. We report that in addition to NDP52/CALCOCO2 and OPTINEURIN/OPTN, another autophagy receptor, namely T6BP/TAXIBP1, also regulates the maturation of autophagosomes by promoting their fusion with lysosomes, independently of any infection. Surprisingly, only two of these receptors, NDP52 and T6BP, impacted measles virus replication, although independently, and possibly through physical interaction with MeV proteins. Thus, our results suggest that a restricted set of autophagosomes is selectively exploited by measles virus to replicate in the course of infection.
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Building a bio-based industry in the Middle East through harnessing the potential of the Red Sea biodiversity

The incentive for developing microbial cell factories for production of fuels and chemicals comes from the ability of microbes to deliver these valuable compounds at a reduced cost and with a smaller environmental impact compared to the analogous chemical synthesis. Another crucial advantage of microbes is their great biological diversity, which offers a much larger “catalog” of molecules than the one obtainable by chemical synthesis. Adaptation to different environments is one of the important drives behind microbial diversity. We argue that the Red Sea, which is a rather unique marine niche, represents a remarkable source of biodiversity that can be geared towards economical and sustainable bioproduction processes in the local area and can be competitive in the international bio-based economy. Recent bioprospecting studies, conducted by the King Abdullah University of Science and Technology, have established important leads on the Red Sea biological potential, with newly isolated strains of Bacilli and Cyanobacteria. We argue that these two groups of local organisms are currently most promising in terms of developing cell factories, due to their ability to operate in saline conditions, thus reducing the cost of desalination and sterilization. The ability of Cyanobacteria to perform photosynthesis can be fully exploited in this particular environment with one of the highest levels of irradiation on the planet. We highlight the importance of new experimental and in silico methodologies needed to overcome the hurdles of developing efficient cell factories from the Red Sea isolates.
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Great New Book - Common Science Space

Great New Book - Common Science Space | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
There’s a great new book about vitamin A, the “vision vitamin”. The title is “Brilliance & Confusion: Saving Children’s Vision & Lives With Vitamin A”. Okay, I confess. It’s my own book, which I just completed (it’s available on Amazon; Kindle version coming soon). One relatively new aspect of this vitamin, which was discovered in 1913 but which has... Continue Reading
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Ten simple rules to make the most out of your undergraduate research career

Ten simple rules to make the most out of your undergraduate research career | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Despite the multiple benefits that research offers, undergraduates sometimes struggle and feel overwhelmed with the research process. Some undergraduates may not be familiar with the dynamics of the lab and may be afraid to interact with their lab colleagues and mentors. Other undergraduates may not completely understand the purpose of their work and feel overwhelmed by not knowing the results of their experiments before performing them. These consequences could, in turn, have detrimental effects on the relationship between undergraduates and their lab colleagues and decrease the motivation for undergraduates to pursue research in the future [4–5]. In light of these concerns, we propose ten simple rules constructed from our experiences as a college senior and a professor who has worked with undergraduate researchers that would help undergraduates enjoy and intellectually enrich their research experiences.
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NCBI researchers and collaborators discover novel group of giant viruses

NCBI researchers and collaborators discover novel group of giant viruses | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
An international team of researchers, including NCBI’s Eugene Koonin and Natalya Yutin, has discovered a novel group of giant viruses (dubbed “Klosneuviruses”) with a more complete set of translation machinery genes than any virus that has been described to date. “This discovery significantly expands our understanding of viral evolution,” said Koonin. “These are the most ‘cell-like’ viruses ever identified. However, the computational analysis of the virus genomes shows that these viruses have not evolved from cells by reductive evolution but rather have evolved from smaller viruses, gradually acquiring genes from their hosts at different stages of their evolution.”


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QuickBLASTP adds pre-processing to BLAST search

QuickBLASTP adds pre-processing to BLAST search | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
QuickBLASTP, an accelerated version of BLASTP, adds a new pre-processing step to the non-redundant (nr) protein database. In a matter of seconds, QuickBLASTP will find approximately 97% of the database sequences with 70% or more identity to your query and around 98% of the database sequence with 80% or more identity to your query.
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Twenty-five lectures in virology for 2017

With the spring semester behind us, this year’s virology lecture series is complete, and videos are available at YouTube.
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