Curation of viral genomes: Challenges, applications and the way forward

Bioinformatics Centre, University of Pune, Pune 411 007 India.
BMC Bioinformatics (Impact Factor: 2.58). 02/2006; 7 Suppl 5(Suppl 5):S12. DOI: 10.1186/1471-2105-7-S5-S12
Source: PubMed


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.
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.
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.

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    • "Curation and annotation of viral [26], bacterial [27] and zebrafish [28] genomes present interesting challenges, due to the range in genome size, variability and complexity. In the case of zebrafish, Christoffels et al. [28] have effectively used carp ESTs to facilitate the annotation. "
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    ABSTRACT: Abstract In 1998, the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able to gain sufficient critical mass to initiate the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2006 Conference was organized as the 5<sup>th </sup>annual conference of the Asia-Pacific Bioinformatics Network, on Dec. 18–20, 2006 in New Delhi, India, following a series of successful events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand) and Busan (South Korea). This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. It exemplifies a typical snapshot of the growing research excellence in bioinformatics of the region as we embark on a trajectory of establishing a solid bioinformatics research culture in the Asia Pacific that is able to contribute fully to the global bioinformatics community.
    BMC Bioinformatics 12/2006; 7(Suppl 5). DOI:10.1186/1471-2105-7-S5-S1 · 2.58 Impact Factor
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    ABSTRACT: It is widely assumed that new proteins are created by duplication, fusion, or fission of existing coding sequences. Another mechanism of protein birth is provided by overlapping genes. They are created de novo by mutations within a coding sequence that lead to the expression of a novel protein in another reading frame, a process called "overprinting." To investigate this mechanism, we have analyzed the sequences of the protein products of manually curated overlapping genes from 43 genera of unspliced RNA viruses infecting eukaryotes. Overlapping proteins have a sequence composition globally biased toward disorder-promoting amino acids and are predicted to contain significantly more structural disorder than nonoverlapping proteins. By analyzing the phylogenetic distribution of overlapping proteins, we were able to confirm that 17 of these had been created de novo and to study them individually. Most proteins created de novo are orphans (i.e., restricted to one species or genus). Almost all are accessory proteins that play a role in viral pathogenicity or spread, rather than proteins central to viral replication or structure. Most proteins created de novo are predicted to be fully disordered and have a highly unusual sequence composition. This suggests that some viral overlapping reading frames encoding hypothetical proteins with highly biased composition, often discarded as noncoding, might in fact encode proteins. Some proteins created de novo are predicted to be ordered, however, and whenever a three-dimensional structure of such a protein has been solved, it corresponds to a fold previously unobserved, suggesting that the study of these proteins could enhance our knowledge of protein space.
    Journal of Virology 08/2009; 83(20):10719-36. DOI:10.1128/JVI.00595-09 · 4.44 Impact Factor
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