Open Access Methodology article

Predicting functional upstream open reading frames in Saccharomyces cerevisiae

Selpi1*, Christopher H Bryant2, Graham JL Kemp3, Janeli Sarv4, Erik Kristiansson5 and Per Sunnerhagen6

Author Affiliations

1 Department of Applied Mechanics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden

2 School of Computing, Science and Engineering, University of Salford, Salford, M5 4WT, UK

3 Department of Computer Science and Engineering, Chalmers University of Technology, SE-412 96 Göteborg, Sweden

4 Department of Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, SE-412 96 Göteborg, Sweden

5 Department of Zoology, University of Gothenburg, Box 463, SE-405 30 Göteborg, Sweden

6 Department of Cell and Molecular Biology, Lundberg Laboratory, University of Gothenburg, PO BOX 462, SE-405 30 Göteborg, Sweden

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BMC Bioinformatics 2009, 10:451  doi:10.1186/1471-2105-10-451

Published: 30 December 2009

Additional files

Additional file 1:

This file consists of four parts. The first part contains the background knowledge, the parameter settings and the definition of hypotheses space for the ILP system used in this study. The second part contains a figure that shows Saccharomyces phylogeny. The third part gives a short description of microarray data analysis. The last part lists the predicted functional uORFs including eleven that our analysis suggests to be strong candidates for wet-lab experimental studies.

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