BMC Genomics 2009, 10:435 http://www.biomedcentral.com/1471-2164/10/435 FAingnuorteat7ion pipeline for human transcribed and conserved pseudogenes Annotation pipeline for human transcribed and conserved pseudogenes. (Note: 'dmRNA' represents disrupted mRNA dataset from ref. [16], 'tppg' represents transcribed processed pseudogenes from ref. [14].) human sequence until the Dnt value was reached; (iii) Ka/ Ks was calculated using PAML [45], for each simulated sequence compared to the original human sequence; (iv) those original human sequences that have Ka/Ks values < 95% of simulated Ka/Ks values were labeled as potentially under significant purifying selection. For these simula- tions, all Ka/Ks calculations are performed on the longest ORF in the sequence. We also analysed simulated distributions of Ka/Ks for populations of sequences mutating without coding- sequence selection pressures, starting from the human TPA sequences. These were derived simply by merging the simulated distributions of Ka/Ks for each individual TPA. 7. Annotation of disrupted protein domains Protein domains were assigned to the TPAs, using protein structure domain sequences downloaded from the ASTRALSCOP database http://astral.berkeley.edu, as described previously [4]. Protein domains sequences were aligned to the TPA nucleotide sequences to assess for dis- ablement by a frameshift or premature stop codon at least Page 12 of 14 (page number not for citation purposes)