BMC Genomics 2009, 10:576 http://www.biomedcentral.com/1471-2164/10/576 Additional file 2 YY1 forward matrix. Position weight matrix file for "matrix-bidirec- tional.pl.txt" named "YY1_F.matrix". Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-576-S2.TXT] Additional file 3 YY1 reverse matrix. Position weight matrix file for "matrix-bidirec- tional.pl.txt" named "YY1_R.matrix". Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-576-S3.MATR] Additional file 4 Dipeptide count Perl program. Perl program "dipep-singlefile.txt.pl" requires fasta formatted input files to generate dipeptide counts. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-576-S4.MATR] Acknowledgements We thank Drs. John Caprio, Mike Hellberg, and Andrew Whitehead for critically reading the manuscript. We also thank the anonymous reviewers for helpful comments. 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