Dataset Information

Filovirus RefSeq entries: evaluation and selection of filovirus type variants, type sequences, and names.

ABSTRACT: Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information's (NCBI's) RefSeq is a non-redundant, curated database for reference (or type) nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [ ()////-], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences.

SUBMITTER: Kuhn JH

PROVIDER: S-EPMC4189044 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature

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Filovirus RefSeq entries: evaluation and selection of filovirus type variants, type sequences, and names.

Kuhn Jens H JH Andersen Kristian G KG Bào Yīmíng Y Bavari Sina S Becker Stephan S Bennett Richard S RS Bergman Nicholas H NH Blinkova Olga O Bradfute Steven S Brister J Rodney JR Bukreyev Alexander A Chandran Kartik K Chepurnov Alexander A AA Davey Robert A RA Dietzgen Ralf G RG Doggett Norman A NA Dolnik Olga O Dye John M JM Enterlein Sven S Fenimore Paul W PW Formenty Pierre P Freiberg Alexander N AN Garry Robert F RF Garza Nicole L NL Gire Stephen K SK Gonzalez Jean-Paul JP Griffiths Anthony A Happi Christian T CT Hensley Lisa E LE Herbert Andrew S AS Hevey Michael C MC Hoenen Thomas T Honko Anna N AN Ignatyev Georgy M GM Jahrling Peter B PB Johnson Joshua C JC Johnson Karl M KM Kindrachuk Jason J Klenk Hans-Dieter HD Kobinger Gary G Kochel Tadeusz J TJ Lackemeyer Matthew G MG Lackner Daniel F DF Leroy Eric M EM Lever Mark S MS Mühlberger Elke E Netesov Sergey V SV Olinger Gene G GG Omilabu Sunday A SA Palacios Gustavo G Panchal Rekha G RG Park Daniel J DJ Patterson Jean L JL Paweska Janusz T JT Peters Clarence J CJ Pettitt James J Pitt Louise L Radoshitzky Sheli R SR Ryabchikova Elena I EI Saphire Erica Ollmann EO Sabeti Pardis C PC Sealfon Rachel R Shestopalov Aleksandr M AM Smither Sophie J SJ Sullivan Nancy J NJ Swanepoel Robert R Takada Ayato A Towner Jonathan S JS van der Groen Guido G Volchkov Viktor E VE Volchkova Valentina A VA Wahl-Jensen Victoria V Warren Travis K TK Warfield Kelly L KL Weidmann Manfred M Nichol Stuart T ST

Viruses 20140926 9

Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characte ...[more]

PMID: 25256396

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Project description:The Electron Microscopy Data Bank (EMDB) is the central archive of the electron cryo-microscopy (cryo-EM) community for storing and disseminating volume maps and tomograms. With input from the community, EMDB has developed new resources for the validation of cryo-EM structures, focusing on the quality of the volume data alone and that of the fit of any models, themselves archived in the Protein Data Bank (PDB), to the volume data. Based on recommendations from community experts, the validation resources are developed in a three-tiered system. Tier 1 covers an extensive and evolving set of validation metrics, including tried and tested metrics as well as more experimental ones, which are calculated for all EMDB entries and presented in the Validation Analysis (VA) web resource. This system is particularly useful for cryo-EM experts, both to validate individual structures and to assess the utility of new validation metrics. Tier 2 comprises a subset of the validation metrics covered by the VA resource that have been subjected to extensive testing and are considered to be useful for specialists as well as nonspecialists. These metrics are presented on the entry-specific web pages for the entire archive on the EMDB website. As more experience is gained with the metrics included in the VA resource, it is expected that consensus will emerge in the community regarding a subset that is suitable for inclusion in the tier 2 system. Tier 3, finally, consists of the validation reports and servers that are produced by the Worldwide Protein Data Bank (wwPDB) Consortium. Successful metrics from tier 2 will be proposed for inclusion in the wwPDB validation pipeline and reports. The details of the new resource are described, with an emphasis on the tier 1 system. The output of all three tiers is publicly available, either through the EMDB website (tiers 1 and 2) or through the wwPDB ftp sites (tier 3), although the content of all three will evolve over time (fastest for tier 1 and slowest for tier 3). It is our hope that these validation resources will help the cryo-EM community to obtain a better understanding of the quality and of the best ways to assess the quality of cryo-EM structures in EMDB and PDB.

Dataset Information

Filovirus RefSeq entries: evaluation and selection of filovirus type variants, type sequences, and names.

Publications

Filovirus RefSeq entries: evaluation and selection of filovirus type variants, type sequences, and names.

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