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EVALLER: a web server for in silico assessment of potential protein allergenicity
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Pharmacology. (Cancer pharmacology and informatics (Rolf Larsson))
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Pharmacology. Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Signals and Systems Group. (Rolf Larsson)
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2007 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 35, W694-W700 p.Article in journal (Refereed) Published
Abstract [en]

Bioinformatics testing approaches for protein allergenicity, involving amino acid sequence comparisons, have evolved appreciably over the last several years to increased sophistication and performance. EVALLER, the web server presented in this article is based on our recently published 'Detection based on Filtered Length-adjusted Allergen Peptides' (DFLAP) algorithm, which affords in silico determination of potential protein allergenicity of high sensitivity and excellent specificity. To strengthen bioinformatics risk assessment in allergology EVALLER provides a comprehensive outline of its judgment on a query protein's potential allergenicity. Each such textual output incorporates a scoring figure, a confidence numeral of the assignment and information on high- or low-scoring matches to identified allergen-related motifs, including their respective location in accordingly derived allergens. The interface, built on a modified Perl Open Source package, enables dynamic and color-coded graphic representation of key parts of the output. Moreover, pertinent details can be examined in great detail through zoomed views. The server can be accessed at http://bioinformatics.bmc.uu.se/evaller.html.

Place, publisher, year, edition, pages
2007. Vol. 35, W694-W700 p.
National Category
Medical and Health Sciences Signal Processing
Research subject
Electrical Engineering with specialization in Signal Processing
Identifiers
URN: urn:nbn:se:uu:diva-99645DOI: 10.1093/nar/gkm370ISI: 000255311500128PubMedID: 17537818OAI: oai:DiVA.org:uu-99645DiVA: diva2:208453
Available from: 2009-03-18 Created: 2009-03-18 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. 103 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 703
Keyword
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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Gustafsson, Mats G.

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