<P> Owing to its greater expediency and speed, dye - terminator sequencing is now the mainstay in automated sequencing . Its limitations include dye effects due to differences in the incorporation of the dye - labelled chain terminators into the DNA fragment, resulting in unequal peak heights and shapes in the electronic DNA sequence trace chromatogram after capillary electrophoresis (see figure to the left). </P> <P> This problem has been addressed with the use of modified DNA polymerase enzyme systems and dyes that minimize incorporation variability, as well as methods for eliminating "dye blobs". The dye - terminator sequencing method, along with automated high - throughput DNA sequence analyzers, is now being used for the vast majority of sequencing projects . </P> <P> Automated DNA - sequencing instruments (DNA sequencers) can sequence up to 384 DNA samples in a single batch . Batch runs may occur up to 24 times a day . DNA sequencers separate strands by size (or length) using capillary electrophoresis, they detect and record dye fluorescence, and output data as fluorescent peak trace chromatograms . Sequencing reactions (thermocycling and labelling), cleanup and re-suspension of samples in a buffer solution are performed separately, before loading samples onto the sequencer . A number of commercial and non-commercial software packages can trim low - quality DNA traces automatically . These programs score the quality of each peak and remove low - quality base peaks (which are generally located at the ends of the sequence). The accuracy of such algorithms is inferior to visual examination by a human operator, but is adequate for automated processing of large sequence data sets . </P> <P> Common challenges of DNA sequencing with the Sanger method include poor quality in the first 15 - 40 bases of the sequence due to primer binding and deteriorating quality of sequencing traces after 700 - 900 bases . Base calling software such as Phred typically provides an estimate of quality to aid in trimming of low - quality regions of sequences . </P>

What chemical reaction is prevented by the incorporation of ddntps into the sequencing reaction