Editing DNA sequencing (section)

==== SOLiD sequencing ====
[[File:Library preparation for the SOLiD platform.svg|right|thumb|Library preparation for the SOLiD platform]]
{{Main|ABI Solid Sequencing}}
[[File:Two-base encoding scheme.pdf|thumb|Two-base encoding scheme. In two-base encoding, each unique pair of bases on the 3' end of the probe is assigned one out of four possible colors. For example, "AA" is assigned to blue, "AC" is assigned to green, and so on for all 16 unique pairs. During sequencing, each base in the template is sequenced twice, and the resulting data are decoded according to this scheme.]]

[[Applied Biosystems]]' (now a [[Life Technologies (Thermo Fisher Scientific)|Life Technologies]] brand) SOLiD technology employs [[sequencing by ligation]]. Here, a pool of all possible oligonucleotides of a fixed length are labeled according to the sequenced position. Oligonucleotides are annealed and ligated; the preferential ligation by [[DNA ligase]] for matching sequences results in a signal informative of the nucleotide at that position. Each base in the template is sequenced twice, and the resulting data are decoded according to the [[2 base encoding]] scheme used in this method. Before sequencing, the DNA is amplified by emulsion PCR. The resulting beads, each containing single copies of the same DNA molecule, are deposited on a glass slide.<ref name="pmid18477713">{{cite journal | vauthors = Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, Johnson SM | title = A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning | journal = Genome Res. | volume = 18 | issue = 7 | pages = 1051–63 | date = July 2008 | pmid = 18477713 | pmc = 2493394 | doi = 10.1101/gr.076463.108 }}</ref> The result is sequences of quantities and lengths comparable to Illumina sequencing.<ref name="pmid18165802"/> This [[sequencing by ligation]] method has been reported to have some issue sequencing palindromic sequences.<ref name="Yu-Feng Huang, Sheng-Chung Chen, Yih-Shien Chiang, Tzu-Han Chen & Kuo-Ping Chiu 2012 S10"/>