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      Complete Genome Sequence of a Common Midwife Toad Virus-Like Ranavirus Associated with Mass Mortalities in Wild Amphibians in the Netherlands

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          Abstract

          A ranavirus associated with mass mortalities in wild water frogs ( Pelophylax spp.) and other amphibians in the Netherlands since 2010 was isolated, and its complete genome sequence was determined. The virus has a genome of 107,772 bp and shows 96.5% sequence identity with the common midwife toad virus from Spain.

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          RATT: Rapid Annotation Transfer Tool

          Second-generation sequencing technologies have made large-scale sequencing projects commonplace. However, making use of these datasets often requires gene function to be ascribed genome wide. Although tool development has kept pace with the changes in sequence production, for tasks such as mapping, de novo assembly or visualization, genome annotation remains a challenge. We have developed a method to rapidly provide accurate annotation for new genomes using previously annotated genomes as a reference. The method, implemented in a tool called RATT (Rapid Annotation Transfer Tool), transfers annotations from a high-quality reference to a new genome on the basis of conserved synteny. We demonstrate that a Mycobacterium tuberculosis genome or a single 2.5 Mb chromosome from a malaria parasite can be annotated in less than five minutes with only modest computational resources. RATT is available at http://ratt.sourceforge.net.
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            Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology

            Motivation: The accuracy of reference genomes is important for downstream analysis but a low error rate requires expensive manual interrogation of the sequence. Here, we describe a novel algorithm (Iterative Correction of Reference Nucleotides) that iteratively aligns deep coverage of short sequencing reads to correct errors in reference genome sequences and evaluate their accuracy. Results: Using Plasmodium falciparum (81% A + T content) as an extreme example, we show that the algorithm is highly accurate and corrects over 2000 errors in the reference sequence. We give examples of its application to numerous other eukaryotic and prokaryotic genomes and suggest additional applications. Availability: The software is available at http://icorn.sourceforge.net Contact: tdo@sanger.ac.uk; cnewbold@hammer.imm.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
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              Ranavirus: past, present and future.

              Emerging infectious diseases are a significant threat to global biodiversity. While historically overlooked, a group of iridoviruses in the genus Ranavirus has been responsible for die-offs in captive and wild amphibian, reptile and fish populations around the globe over the past two decades. In order to share contemporary information on ranaviruses and identify critical research directions, the First International Symposium on Ranaviruses was held in July 2011 in Minneapolis, MN, USA. Twenty-three scientists and veterinarians from nine countries examined the ecology and evolution of ranavirus-host interactions, potential reservoirs, transmission dynamics, as well as immunological and histopathological responses to infection. In addition, speakers discussed possible mechanisms for die-offs, and conservation strategies to control outbreaks.
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                Author and article information

                Journal
                Genome Announc
                Genome Announc
                ga
                ga
                GA
                Genome Announcements
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2169-8287
                24 December 2014
                Nov-Dec 2014
                : 2
                : 6
                : e01293-14
                Affiliations
                [a ]Faculty of Veterinary Medicine, Utrecht University, the Netherlands
                [b ]MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
                [c ]Dutch Wildlife Health Centre, Utrecht, the Netherlands
                [d ]Central Veterinary Institute, Wageningen UR, Lelystad, the Netherlands
                Author notes
                Address correspondence to Steven J. van Beurden, s.j.vanbeurden@ 123456uu.nl .
                Article
                genomeA01293-14
                10.1128/genomeA.01293-14
                4276818
                25540340
                19671b8d-9747-429e-ac93-bfe5170c0293
                Copyright © 2014 van Beurden et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.

                History
                : 7 November 2014
                : 19 November 2014
                Page count
                Pages: 2
                Categories
                Viruses
                Custom metadata
                November/December 2014
                free

                Genetics
                Genetics

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