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      Complete Coding Sequence of a Lumpy Skin Disease Virus from an Outbreak in Bulgaria in 2016

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          Abstract

          Lumpy skin disease (LSD) is an emerging cattle disease with serious economic consequences. We report the complete coding sequence of LSD virus 210LSD-249/BUL/16, detected in a blood sample from a diseased cow during an outbreak in Bulgaria (Kabile Village, Yambol Region) in June 2016.

          ABSTRACT

          Lumpy skin disease (LSD) is an emerging cattle disease with serious economic consequences. We report the complete coding sequence of LSD virus 210LSD-249/BUL/16, detected in a blood sample from a diseased cow during an outbreak in Bulgaria (Kabile Village, Yambol Region) in June 2016.

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          SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

          Anton Bankevich, Sergey Nurk, Dmitry Antipov … (2012)
          The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
          Article 0 comments Cited 6233 times – based on 0 reviews     Review now
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            NCBI BLAST: a better web interface

            Mark Johnson, Irena Zaretskaya, Yan Raytselis … (2008)
            Basic Local Alignment Search Tool (BLAST) is a sequence similarity search program. The public interface of BLAST, http://www.ncbi.nlm.nih.gov/blast, at the NCBI website has recently been reengineered to improve usability and performance. Key new features include simplified search forms, improved navigation, a list of recent BLAST results, saved search strategies and a documentation directory. Here, we describe the BLAST web application's new features, explain design decisions and outline plans for future improvement.
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              Genome Annotation Transfer Utility (GATU): rapid annotation of viral genomes using a closely related reference genome

              Vasily Tcherepanov, Angelika Ehlers, Chris Upton (2006)
              Background Since DNA sequencing has become easier and cheaper, an increasing number of closely related viral genomes have been sequenced. However, many of these have been deposited in GenBank without annotations, severely limiting their value to researchers. While maintaining comprehensive genomic databases for a set of virus families at the Viral Bioinformatics Resource Center and Viral Bioinformatics – Canada , we found that researchers were unnecessarily spending time annotating viral genomes that were close relatives of already annotated viruses. We have therefore designed and implemented a novel tool, Genome Annotation Transfer Utility (GATU), to transfer annotations from a previously annotated reference genome to a new target genome, thereby greatly reducing this laborious task. Results GATU transfers annotations from a reference genome to a closely related target genome, while still giving the user final control over which annotations should be included. GATU also detects open reading frames present in the target but not the reference genome and provides the user with a variety of bioinformatics tools to quickly determine if these ORFs should also be included in the annotation. After this process is complete, GATU saves the newly annotated genome as a GenBank, EMBL or XML-format file. The software is coded in Java and runs on a variety of computer platforms. Its user-friendly Graphical User Interface is specifically designed for users trained in the biological sciences. Conclusion GATU greatly simplifies the initial stages of genome annotation by using a closely related genome as a reference. It is not intended to be a gene prediction tool or a "complete" annotation system, but we have found that it significantly reduces the time required for annotation of genes and mature peptides as well as helping to standardize gene names between related organisms by transferring reference genome annotations to the target genome. The program is freely available under the General Public License and can be accessed along with documentation and tutorial from .
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                Author and article information

                Contributors
                Jelle Matthijnssens: Role: Editor
                Journal
                Journal ID (nlm-ta): Microbiol Resour Announc
                Journal ID (iso-abbrev): Microbiol Resour Announc
                Journal ID (hwp): ga
                Journal ID (pmc): mra
                Journal ID (publisher-id): MRA
                Title: Microbiology Resource Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2576-098X
                Publication date (Electronic): 22 October 2020
                Publication date Collection: October 2020
                Volume: 9
                Issue: 43
                Electronic Location Identifier: e00977-20
                Affiliations
                [a ]Sciensano, EURL Capripox, Unit Exotic Viruses and Particular Diseases, Ukkel, Belgium
                [b ]National Diagnostic and Research Veterinary Medical Institute, Sofia, Bulgaria
                KU Leuven
                Author notes
                Address correspondence to Elisabeth Mathijs, elisabeth.mathijs@ 123456sciensano.be .

                Citation Mathijs E, Vandenbussche F, Ivanova E, Haegeman A, Aerts L, De Leeuw I, Van Borm S, De Clercq K. 2020. Complete coding sequence of a lumpy skin disease virus from an outbreak in Bulgaria in 2016. Microbiol Resour Announc 9:e00977-20. https://doi.org/10.1128/MRA.00977-20.

                Author information
                https://orcid.org/0000-0001-6004-605X
                Article
                Publisher ID: MRA00977-20
                DOI: 10.1128/MRA.00977-20
                PMC ID: 7585842
                PubMed ID: 33093046
                SO-VID: 612764d3-a941-4836-bfea-0ca74fe648b5
                Copyright © Copyright © 2020 Mathijs et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Date received : 21 August 2020
                Date accepted : 25 September 2020
                Page count
                Figures: 0, Tables: 1, Equations: 0, References: 9, Pages: 2, Words: 1257
                Categories
                Subject: Genome Sequences
                Custom metadata
                cover-date October 2020

                Data availability:

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