uu.seUppsala University Publications
Change search
ReferencesLink to record
Permanent link

Direct link
Approaching a unified data processing model for oligonucleotide design
Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
Manuscript (Other academic)
URN: urn:nbn:se:uu:diva-94412OAI: oai:DiVA.org:uu-94412DiVA: diva2:168250
Available from: 2006-05-02 Created: 2006-05-02 Last updated: 2010-01-13Bibliographically approved
In thesis
1. Software Tools for Design of Reagents for Multiplex Genetic Analyses
Open this publication in new window or tab >>Software Tools for Design of Reagents for Multiplex Genetic Analyses
2006 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Methods using oligonucleotide probes are powerful tools for the analysis of nucleic acids. During recent years, many such methods have been developed that enable the simultaneous interrogation of multiple qualities of a sample. Many of these multiplexing techniques share common limitations. This thesis discusses new developments to overcome the problems of multiplex amplification of genomic sequences and design of sets of oligonucleotide probes for multiplex genetic analyses.

A novel molecular technique, termed the selector method, is described. This method allows circularization of an arbitrary selection of restriction fragments from genomic DNA, and the subsequent amplification of these circular products in parallel using common primers. The utility of the method is demonstrated by a 96-plex amplification experiment. Furthermore, the PieceMaker software for selection of restriction enzymes and restriction fragments is described. These two developments allow the selective amplification of subsets of genomes for further analyses.

A software tool for the design of sequence-tagged oligonucleotide probes is presented. The ProbeMaker software is a framework for design of sets of probes composed of separate functional elements, and uses an extension mechanism to incorporate support for new probe types as needed. An approach to a unified system for oligonucleotide design is also presented. This system will serve to decrease development times for new oligonucleotide design applications by allowing extensive code reuse.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2006. 41 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 148
Bioinformatics, Bioinformatik
urn:nbn:se:uu:diva-6832 (URN)91-554-6551-X (ISBN)
Public defence
2006-05-23, Rudbecksalen, Rudbecklaboratoriet, Dag Hammarskjölds väg 20, Uppsala, 09:15
Available from: 2006-05-02 Created: 2006-05-02Bibliographically approved

Open Access in DiVA

No full text

By organisation
Department of Genetics and Pathology

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Total: 172 hits
ReferencesLink to record
Permanent link

Direct link