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GeneFinder: "in silico" positional cloning of trait genes
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics. (Bongcam-Rudloff)
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences. (Bongcam-Rudloff)
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences. (Bongcam-Rudloff)
(English)Manuscript (preprint) (Other (popular science, discussion, etc.))
Abstract [en]

Motivation: Positional cloning of trait genes is extremely laborious and the amount of information available on gene function in different organisms is increasing so rapidly that it is hard for a research group to collect all the relevant information from a number of data sources without performing a large number of manual and time consuming searches.

Results: A web service application named GeneFinder was designed and implemented. It collects selected available information related to trait loci within a given chromosomal region that control a specific phenotype. The information contains details on gene function, disease conditions, tissue expression as well as predicted gene homologies in several other species. The information gathered is further ordered by a special-purpose ranking algorithm. A web interface to the GeneFinder web service was also developed where the results are presented in a ranked list easing its interpretation. We explain the design of the architecture, show how our web interface works, and finally test a candidate region.

Availability: GeneFinder is publicly available and free to use. The web interface is available at http://www.genefinder.org/.

Keyword [en]
data integration, web services, GWAS, genome-wide association studies
National Category
Medical Genetics Bioinformatics and Systems Biology
Research subject
Medical Genetics
Identifiers
URN: urn:nbn:se:uu:diva-112124OAI: oai:DiVA.org:uu-112124DiVA: diva2:284978
Projects
EMBRACE
Available from: 2010-01-09 Created: 2010-01-09 Last updated: 2010-01-11
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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Martinez Barrio, Alvaro

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