Croning et al. BMC Genomics 2010, 11:74 http://www.biomedcentral.com/1471-2164/11/74 [ http://www.biomedcentral.com/content/supplementary/1471-2164-11- 74-S1.GZ ] Abbreviations API: application programming interface; BLAST: basic local alignment search tool; bp: base pairs; DNA: deoxyribonucleic acid; kb: kilobase; LSF: load sharing facility; PCR: polymerase chain reaction; SQL: structured query language. Acknowledgements Funding: Wellcome Trust The authors wish to thank Drs Louie N. van de Lagemaat, René Frank and Rob Andrews for their critical reading of an earlier version of the manuscript. Authors’ contributions MDRC conceived and implemented the method. DGF experimentally validated the resulting probes. NHK and SGNG directed the investigation. All authors read and approved the final manuscript. Received: 28 October 2009 Accepted: 29 January 2010 Published: 29 January 2010 References 1. Southern EM: Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 1975, 98(3):503-517. 2. Grant SG, Jessee J, Bloom FR, Hanahan D: Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. Proc Natl Acad Sci USA 1990, 87(12):4645-4649. 3. Komiyama NH, Watabe AM, Carlisle HJ, Porter K, Charlesworth P, Monti J, Strathdee DJ, O’Carroll CM, Martin SJ, Morris RG, et al: SynGAP regulates ERK/MAPK signaling, synaptic plasticity, and learning in the complex with postsynaptic density 95 and NMDA receptor. J Neurosci 2002, 22(22):9721-9732. 4. Sambrook J, Russell DW: Molecular Cloning A Laborarory Manual. New York: Coldspring Harbour Laboratory Press, third 2001, 1. 5. Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, et al: Ensembl 2009. Nucleic Acids Res 2009, , 37 Database: D690-697. 6. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410. 7. Li F, Stormo GD: Selection of optimal DNA oligos for gene expression arrays. Bioinformatics 2001, 17(11):1067-1076. 8. Slater GS, Birney E: Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 2005, 6:31. 9. RepeatMasker Open-3.0. http://www.repeatmasker.org. 10. Morgulis A, Gertz EM, Schaffer AA, Agarwala R: A fast and symmetric DUST implementation to mask low-complexity DNA sequences. J Comput Biol 2006, 13(5):1028-1040. 11. Stabenau A, McVicker G, Melsopp C, Proctor G, Clamp M, Birney E: The Ensembl core software libraries. Genome Res 2004, 14(5):929-933. 12. Rozen SaS HJ: Primer3 on the WWW for general users and for biologist programmers. Bioinformatics Methods and Protocols: Methods in Molecular Biology Towota, NJ: Humana PressKrawetz SaMS 2000, 365-386. 13. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, et al: The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002, 12(10):1611-1618. 14. Grant SG: Systems biology in neuroscience: bridging genes to cognition. Curr Opin Neurobiol 2003, 13(5):577-582. doi:10.1186/1471-2164-11-74 Cite this article as: Croning et al.: Automated design of genomic Southern blot probes. BMC Genomics 2010 11:74. Page 7 of 7 Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review • No space constraints or color ﬁgure charges • Immediate publication on acceptance • Inclusion in PubMed, CAS, Scopus and Google Scholar • Research which is freely available for redistribution Submit your manuscript at www.biomedcentral.com/submit