BMC Genomics 2008, 9:122 http://www.biomedcentral.com/1471-2164/9/122 Sequence annotation, such as the number of introns, flanking genomic sequence and SNP data, was extracted from Ensembl [33,34], and multiple sequence alignments generated with CLUSTAL W v. 1.83 [35,36]. To verify whether the THPO matreshka start is associated with a transcription start site, the program Eponine was used, available from the Sanger Center web site [37]. Authors' contributions SR implemented and ran the computational analysis, and drafted the manuscript. AB implemented the ORF extrac- tion and alignment software used, and advised on strat- egy. BB advised on data analysis and assisted with manuscript preparation. KS advised on strategy and par- ticipated in coordination. MRJ conceived and designed the study, and participated in coordination. All authors proofread and approved the final manuscript. Additional material Additional file 1 Bi-codon frequencies Click here for file 2164-9-122-S1.xls] Additional file 2 2164-9-122-S2.doc] Additional file 3 [http://www.biomedcentral.com/content/supplementary/1471- Frameshifted splice variants. Human frameshifted PAX8, XBP1 and CASP7 splice variants which contain matreshka sequences. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- Matreshka characteristics. data on all matreshkas, including sequence identifiers, lengths and number of potential stop codons. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-9-122-S3.xls] Additional file 4 Matreshka overlap with ARFs. Table of genes containing alternative reading frames [8] which are represented in the matreshka set. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-9-122-S4.doc] Additional file 5 Fasta format. Click here for file 2164-9-122-S5.txt] MatreshkaM sequences. Human matreshkaM nucleotide sequences in [http://www.biomedcentral.com/content/supplementary/1471- Additional file 6 format. MatreshkaX sequences. Human matreshkaX nucleotide sequences in Fasta Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-9-122-S6.txt] Acknowledgements Research, Basel, Switzerland. References This study was entirely funded by the Novartis Institutes for Biomedical 1. Sharpless NE, DePinho RA: The INK4A/ARF locus and its two gene products. Current Opinion in Genetics & Development 1999, 9(1):22-30. 2. Poulin F, Brueschke A, Sonenberg N: Gene Fusion and Overlap- ping Reading Frames in the Mammalian Genes for 4E-BP3 and MASK. J Biol Chem 2003, 278(52):52290-52297. 3. Hameed M, Orrell RW, Cobbold M, Goldspink G, Harridge SDR: Expression of IGF-I splice variants in young and old human skeletal muscle after high resistance exercise. J Physiol 2003, 547(1):247-254. 4. 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