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Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics. (Erik Bongcam)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Physiology. (Sperber)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Virology. (Blomberg)
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2009 (English)In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 10 Suppl. 6, p. S18-Article in journal (Refereed) Published
Abstract [en]

BACKGROUND: The Distributed Annotation System (DAS) is a widely used network protocol for sharing biological information. The distributed aspects of the protocol enable the use of various reference and annotation servers for connecting biological sequence data to pertinent annotations in order to depict an integrated view of the data for the final user. RESULTS: An annotation server has been devised to provide information about the endogenous retroviruses detected and annotated by a specialized in silico tool called RetroTector. We describe the procedure to implement the DAS 1.5 protocol commands necessary for constructing the DAS annotation server. We use our server to exemplify those steps. Data distribution is kept separated from visualization which is carried out by eBioX, an easy to use open source program incorporating multiple bioinformatics utilities. Some well characterized endogenous retroviruses are shown in two different DAS clients. A rapid analysis of areas free from retroviral insertions could be facilitated by our annotations. CONCLUSION: The DAS protocol has shown to be advantageous in the distribution of endogenous retrovirus data. The distributed nature of the protocol is also found to aid in combining annotation and visualization along a genome in order to enhance the understanding of ERV contribution to its evolution. Reference and annotation servers are conjointly used by eBioX to provide visualization of ERV annotations as well as other data sources. Our DAS data source can be found in the central public DAS service repository, http://www.dasregistry.org, or at http://loka.bmc.uu.se/das/sources.

Place, publisher, year, edition, pages
BioMed Central , 2009. Vol. 10 Suppl. 6, p. S18-
National Category
Medical and Health Sciences
Identifiers
URN: urn:nbn:se:uu:diva-106783DOI: 10.1186/1471-2105-10-S6-S18ISI: 000267522200018PubMedID: 19534743OAI: oai:DiVA.org:uu-106783DiVA, id: diva2:226647
Available from: 2009-07-03 Created: 2009-07-02 Last updated: 2017-12-13Bibliographically approved
In thesis
1. Novel Bioinformatics Applications for Protein Allergology, Genome-Wide Association and Retrovirology Studies
Open this publication in new window or tab >>Novel Bioinformatics Applications for Protein Allergology, Genome-Wide Association and Retrovirology Studies
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Recently, the pace of growth in the amount of data sources within Life Sciences has increased exponentially until pose a difficult problem to efficiently manage their integration. The data avalanche we are experiencing may be significant for a turning point in science, with a change of orientation from proprietary to publicly available data and a concomitant acceptance of studies based on the latter. To investigate these issues, a Network of Excellence (EMBRACE) was launched with the aim to integrate the major databases and the most popular bioinformatics software tools. The focus of this thesis is therefore to approach the problem of seamlessly integrating varied data sources and/or distributed research tools.

In paper I, we have developed a web service to facilitate allergenicity risk assessment, based on allergen descriptors, in order to characterize proteins with the potential for sensitization and cross-reactivity.

In paper II, a web service was developed which uses a lightweight protocol to integrate human endogenous retrovirus (ERV) data within a public genome browser. This new data catalogue and many other publicly available sources were integrated and tested in a bioinformatics-rich client application.

In paper III, GeneFinder, a distributed tool for genome-wide association studies, was developed and tested. Useful information based on a particular genomic region can be easily retrieved and assessed.

Finally, in paper IV, we developed a prototype pipeline to mine the dog genome for endogenous retroviruses and displaying the transcriptional landscape of these retroviral integrations. Moreover, we further characterized a group that until this point was believed to be primate-specific. Our results also revealed that the dog has been very effective in protecting itself from such integrations.

This work integrates different applications in the fields of protein allergology, biotechnology, genome association studies and endogenous retroviruses.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2010. p. 103
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 703
Keywords
data integration, web services, protein allergology, risk assessment, cross reactivity, endogenous retroviruses, ERV, dog, canine, GWAS, genome-wide association studies
Identifiers
urn:nbn:se:uu:diva-111932 (URN)978-91-554-7694-6 (ISBN)
Public defence
2010-01-29, C8:301, BMC, Husargatan 3, Uppsala, 09:30 (English)
Opponent
Supervisors
Projects
EMBRACE NoE EU FP6
Available from: 2010-01-08 Created: 2009-12-31 Last updated: 2010-01-11Bibliographically approved

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