PeakPicker software developed for quantitative allele ratio analysis. (A) PeakPicker allows parallel viewing of sequence traces. The three traces shown are illustrating analysis of rs4015375 (STEAP); the top trace represents genomic DNA with a clear heterozygous (C/G) genotype (red arrow); the two traces below show the independent replicates of the corresponding RNA samples, in which predominant expression of one allele (G) is evident. (B) Multiple alignment is carried out and samples passing the user-defined alignment score (% match) are analyzed further. (C) A reference sequence (typically one of the genomic DNA controls) is used to select SNP and control peaks. (D) PeakPicker identifies the SNP and control peaks in all sequences analyzed in parallel and generates a table flagging suspicious values to allow manual review of peak selection. (E) A text file with SNP allele ratios normalized based on the control peaks is generated as an output.