BMC Genomics 2009, 10:435 http://www.biomedcentral.com/1471-2164/10/435 15 amino acids from the end of the aligned subsequence. Disablements were required to be detected both by blast/ bl2seq and by the TFASTX program [4,39]. 8. Antisense homology Transcribed human pseudogenes were aligned to full- length annotated human cDNA to examine for any anti- sense homology by using the sequence-searching program BlastN from the BLAST package (E-value < 1e-10). 9. small RNA (siRNA) mapping siRNAs have been previously determined in the mouse genome [18,19]. Using this data we mapped the siRNA sequences onto the mouse genome using GMAP software [41], and checked how many of these overlap with the annotations of transcribed mouse pseudogenes. 10. Phylogenetic analysis Ortholog sequences to the human transcribed ADP-ribose pyrophosphatase pseudogene (urn:lsid:pseudog- ene.org:9606.Pseudogene:4346; see Table 1), were obtained from the various studied mammals and were aligned using the online ClustalW tool http:// www.ebi.ac.uk/clustalw/. The most conserved segment representing 257-396 positions of the human pseudogene was considered for the phylogenetic analysis. Phyloge- netic tree was constructed using 'PHYLIP' software [46]. The tree was evaluated statistically using 1000 bootstrap iterations and was visualized using the 'NJplot' tool [47]. Additional material Additional file 1 List of transcribed human pseudogenes. Genomic coordinates of the transcribed pseudogenes found in the human genome. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-435-S1.xls] Additional file 2 Click here for file Table S2. List of human TPAs that are conserved in other mammals. 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