About: Curation of viral genomes: challenges, applications and the way forward

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Curation of viral genomes: challenges, applications and the way forward
Creator	Bansode, Sandeep Joshi, Manali Kulkarni-Kale, Urmila Bhosle, Shriram Kolaskar, Ashok »more»
source	Medline; PMC
abstract	BACKGROUND: Whole genome sequence data is a step towards generating the 'parts list' of life to understand the underlying principles of Biocomplexity. Genome sequencing initiatives of human and model organisms are targeted efforts towards understanding principles of evolution with an application envisaged to improve human health. These efforts culminated in the development of dedicated resources. Whereas a large number of viral genomes have been sequenced by groups or individuals with an interest to study antigenic variation amongst strains and species. These independent efforts enabled viruses to attain the status of 'best-represented taxa' with the highest number of genomes. However, due to lack of concerted efforts, viral genomic sequences merely remained as entries in the public repositories until recently. RESULTS: VirGen is a curated resource of viral genomes and their analyses. Since its first release, it has grown both in terms of coverage of viral families and development of new modules for annotation and analysis. The current release (2.0) includes data for twenty-five families with broad host range as against eight in the first release. The taxonomic description of viruses in VirGen is in accordance with the ICTV nomenclature. A well-characterised strain is identified as a 'representative entry' for every viral species. This non-redundant dataset is used for subsequent annotation and analyses using sequenced-based Bioinformatics approaches. VirGen archives precomputed data on genome and proteome comparisons. A new data module that provides structures of viral proteins available in PDB has been incorporated recently. One of the unique features of VirGen is predicted conformational and sequential epitopes of known antigenic proteins using in-house developed algorithms, a step towards reverse vaccinology. CONCLUSION: Structured organization of genomic data facilitates use of data mining tools, which provides opportunities for knowledge discovery. One of the approaches to achieve this goal is to carry out functional annotations using comparative genomics. VirGen, a comprehensive viral genome resource that serves as an annotation and analysis pipeline has been developed for the curation of public domain viral genome data . Various steps in the curation and annotation of the genomic data and applications of the value-added derived data are substantiated with case studies.
has issue date	2006-12-18(xsd:dateTime)
bibo:doi	10.1186/1471-2105-7-s5-s12
bibo:pmid	17254296
has license	cc-by
sha1sum (hex)	bd9162d8379baef31b50aa17a7f553740aa28ba2
schema:url	https://doi.org/10.1186/1471-2105-7-s5-s12
resource representing a document's title	Curation of viral genomes: challenges, applications and the way forward
has PubMed Central identifier	PMC1764468
has PubMed identifier	17254296
schema:publication	BMC Bioinformatics
resource representing a document's body	covid:bd9162d8379baef31b50aa17a7f553740aa28ba2#body_text
is schema:about of	named entity 'application' named entity 'model organisms' named entity 'TARGETED' named entity 'DEVELOPMENT' named entity 'IS A' »more»

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