PAGE 15 OF 16 SUPPLEMENTARY MATERIAL Supplementary Material is available at NAR Online. ACKNOWLEDGEMENTS Tampere Graduate School in Information Science and Engineering, the Academy of Finland, and the Medical Research Fund of Tampere University Hospital are acknowl- edged for financial support. Funding to pay the Open Access publication charges for this article was provided by the Academy of Finland. Conflict of interest statement. None declared. REFERENCES 1. Rychlik,W. and Rhoads,R.E. (1989) A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA. Nucleic Acids Res., 17, 8543–8551. 2. Hillier,L. and Green,P. (1991) OSP: a computer program for choosing PCR and DNA sequencing primers. PCR Methods Appl., 1, 124–128. 3. Cutichia,A., Arnold,J. and Timberlake,W.E. (1993) PCAP: probe choice and analysis package—a set of programs to aid in choosing synthetic oligomers for contig mapping. Comput. Appl. Biosci., 9, 201–203. 4. Li,P., Kupfer,K.C., Davies,C.J., Burbee,D., Evans,G.A. and Garner,H.R. (1997) PRIMO: a primer design program that applies base quality statistics for automated large-scale DNA sequencing. Genomics, 40, 476–485. 5. Mecklenburg,M. (1997) Design of high-annealing-temperature primers for PCR and development of a versatile low-copy-number amplification protocol. Adv. Mol. Cell Biol., 15B, 473–490. 6. Haas,S., Vingron,M., Poutska,A. and Wiemann,S. (1998) Primer design for large scale sequencing. Nucleic Acids Res., 26, 3006–3012. 7. Rozen,S. and Skaletsky,H. (1998) Primer3 code. 8. Herwig,R., Schmitt,A.O., Steinfath,M., O’Brian,J., Seidel,H., Meier-Ewert,S., Lehrach,H. and Radelof,U. (2000) Information theoretical probe selection for hybridisation experiments. Bioinformatics, 10, 890–898. 9. Emrich,S.J., Love,M. and Delcher,A.L. (2003) PROBEmer: a web-based software tool for selecting optimal DNA oligos. Nucleic Acids Res., 31, 3746–3750. 10. Chen,S.H., Lin,C.Y., Cho,C.S., Lo,C.Z. and Hsiung,C.A. (2003) Primer Design Assistant (PDA): a web-based primer design tool. Nucleic Acids Res., 31, 3751–3754. 11. van Baren,M.J. and Heutink,P. (2004) The PCR suite. Bioinformatics, 20, 591–593. 12. Jarman,S.N. (2004) Amplicon: software for designing PCR primers on aligned DNA sequences. Bioinformatics, 20, 1644–1645. 13. Wu,J.S., Lee,C., Wu,C.C. and Shiue,Y.L. (2004) Primer design using genetic algorithm. Bioinformatics, 20, 1710–1717. 14. Ka¨mpke,T., Kieninger,M. and Mecklenburg,M. (2001) Efficient primer design algorithms. Bioinformatics, 17, 214–225. 15. Podowski,R.M. and Sonnhammer,E.L. (2001) MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs. Bioinformatics, 17, 656–657. 16. Borneman,J., Chrobak,M., Della Vedova,G., Figueroa,A. and Jiang,T. (2001) Probe selection algorithms with applications in the analysis of microbial communities. Bioinformatics, 17, S39–S48. 17. Kaderali,L. and Schliep,A. (2002) Selecting signature oligonucleotides to identify organisms using DNA arrays. Bioinformatics, 18, 1340–1349. 18. Talaat,A.M., Hunter,P. and Johnston,S.A. (2000) Genome-directed primers for selective labeling of bacterial transcripts for DNA microarray analysis. Nat. Biotechnol., 18, 679–682. 19. Li,F. and Stormo,G. (2001) Selection of optimal DNA oligos for gene expression arrays. Bioinformatics, 17, 1067–1076. Nucleic Acids Research, 2005, Vol. 33, No. 13 e115 20. Raddatz,G., Dehio,M., Meyer,F.T. and Dehio,C. (2001) PrimeArray: genome-scale primer design for DNA-microarray construction. Bioinformatics, 17, 98–99. 21. Nielsen,H.B. and Knudsen,S. (2002) Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays. Bioinformatics, 18, 321–322. 22. Rouillard,J.M., Herbert,C.J. and Zuker,M. (2002) OligoArray: genome-scale oligonucleotide design for microarrays. Bioinformatics, 18, 486–487. 23. Xu,D., Li,G., Wu,L., Zhou,J. and Xu,Y. (2002) PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis. Bioinformatics, 18, 1432–1437. 24. Blick,R.J., Revel,A.T. and Hansen,E.J. (2003) FindGDPs: identification of primers for labeling microbial transcriptomes for DNA microarray analysis. Bioinformatics, 19, 1718–1719. 25. Mei,R., Hubbell,E., Bekiranov,S., Mittmann,M., Christians,F.C., Shen,M.M., Lu,G., Fang,J., Liu,W.M., Ryder,T. et al. (2003) Probe selection for high-density oligonucleotide arrays. Proc. Natl Acad. Sci. USA, 100, 11237–11242. 26. Thareau,V., Dehais,P., Serizet,C., Hilson,P., Rouze,P. and Aubourg,S. (2003) Automatic design of gene-specific sequence tags for genome-wide functional studies. Bioinformatics, 19, 2191–2198. 27. Tolstrup,N., Nielsen,P.S., Kolberg,J.G., Frankel,A.M., Vissing,H. and Kauppinen,S. (2003) OligoDesign: optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling. Nucleic Acids Res., 31, 3758–3762. 28. Wang,X. and Seed,B. (2003) Selection of oligonucleotide probes for protein coding sequences. Bioinformatics, 19, 796–802. 29. Chou,H.H., Hsia,A.P., Mooney,D.L. and Schnable,P.S. (2004) Picky: oligo microarray design for large genomes. Bioinformatics, 20, 2893–2902. 30. Hornshøj,H., Stengaard,H., Panitz,F. and Bendixen,C. (2004) SEPON, a selection and evaluation pipeline for oligonucleotides based on ESTs with a non-target Tm algorithm for reducing cross-hybridization in microarray gene expression experiments. Bioinformatics, 20, 428–429. 31. Reymond,N., Charles,H., Duret,L., Calevro,F., Beslon,G. and Fayard,J.M. (2004) ROSO: optimizing oligonucleotide probes for microarrays. Bioinformatics, 20, 271–273. 32. Sczakiel,G. (2000) Theoretical and experimental approaches to design effective antisense oligonucleotides. Front. Biosci., 5, D194–D201. 33. Toschi,N. (2000) Influence of mRNA self-structure of hybridisation: computational tools for antisense sequence selection. Methods, 22, 261–269. 34. Vickers,T.A., Wyatt,J.R. and Freier,S.M. (2000) Effects of RNA secondary structure on cellular antisense activity. Nucleic Acids Res., 28, 1340–1347. 35. Ding,Y. and Lawrence,C.E. (2001) Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond. Nucleic Acids Res., 29, 1034–1046. 36. Far,R.K., Nedbal,W. and Sczakiel,G. (2001) Concepts to automate the theoretical design of effective antisense oligonucleotides. Bioinformatics, 17, 1058–1061. 37. Chalk,A.M., Wahlestedt,C. and Sonnhammer,E.L. (2004) Improved and automated prediction of effective siRNA. Biochem. Biophys. Res. Commun., 319, 264–274. 38. Levenkova,N., Gu,Q. and Rux,J.J. (2004) Gene specific siRNA selector. Bioinformatics, 20, 430–432. 39. Pancoska,P., Moravek,Z. and Moll,U.M. (2004) Efficient RNA interference depends on global context of the target sequence: quantitative analysis of silencing efficiency using Eulerian graph representation of siRNA. Nucleic Acids Res., 32, 1469–1479. 40. Reynolds,A., Leake,D., Boese,Q., Scaringe,S., Marshall,W.S. and Khvorova,A. (2004) Rational siRNA design for RNA interference. Nat. Biotechnol., 22, 326–330. 41. Wang,L. and Mu,F.Y. (2004) A web-based design center for vector-based siRNA and siRNA cassette. Bioinformatics, 20, 1818–1820. 42. Hoover,D.M. and Lubkowski,J. (2002) DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis. Nucleic Acids Res., 30, e43. 43. Lu,G., Hallett,M., Pollock,S. and Thomas,D. (2003) DePIE: designing primers for protein interaction experiments. Nucleic Acids Res., 31, 3755–3757.