Peak height pattern in dichloro-rhodamine and energy transfer dye terminator sequencing - PubMed (original) (raw)

. 1998 Sep;25(3):406-10, 412-4.

doi: 10.2144/98253st01.

Affiliations

• PMID: 9762437
• DOI: 10.2144/98253st01

Free article

Peak height pattern in dichloro-rhodamine and energy transfer dye terminator sequencing

H Zakeri et al. Biotechniques. 1998 Sep.

Free article

Abstract

Establishing the pattern in peak heights within local sequence contexts improves the accuracy of base calling and the identification of DNA sequence variations in dye-terminator cycle sequencing. We have systematically examined pairs of sequence-tagged sites (STSs) that vary at only a single nucleotide to determine how base changes influence the peak heights of neighboring bases in sequencing traces generated by two recently commercialized dye-terminator chemistries, the dichloro-rhodamine (dRhodamine) and the energy transfer (BigDye) terminators. For sequencing traces generated with the dRhodamine terminators, the peak height of a particular base in 28 of 64 possible 3-base windows (44%) can be predicted by knowing just one or two bases 5' to the base in question. For those generated with the BigDye terminators, the peak height of a particular base in 23 of 64 possible 3-base windows (36%) can be predicted by knowing the local sequence context. When the peak heights are binned slightly differently, 75% (48 out of 64 cases) of the base peaks generated by both dRhodamine and BigDye terminators fall in the middle half, confirming that the peak patterns of these two new dye terminator chemistries are much more even than those found in the original rhodamine dye terminator sequences.

PubMed Disclaimer

Similar articles

• New dye-labeled terminators for improved DNA sequencing patterns.
  Rosenblum BB, Lee LG, Spurgeon SL, Khan SH, Menchen SM, Heiner CR, Chen SM. Rosenblum BB, et al. Nucleic Acids Res. 1997 Nov 15;25(22):4500-4. doi: 10.1093/nar/25.22.4500. Nucleic Acids Res. 1997. PMID: 9358158 Free PMC article.
• AmpliTaq DNA polymerase, FS dye-terminator sequencing: analysis of peak height patterns.
  Parker LT, Zakeri H, Deng Q, Spurgeon S, Kwok PY, Nickerson DA. Parker LT, et al. Biotechniques. 1996 Oct;21(4):694-9. doi: 10.2144/96214rr02. Biotechniques. 1996. PMID: 8891223
• Manganese citrate improves base-calling accuracy in DNA sequencing reactions using rhodamine-based fluorescent dye-terminators.
  Korch C, Drabkin H. Korch C, et al. Nucleic Acids Res. 1999 Mar 1;27(5):1405-7. doi: 10.1093/nar/27.5.1405. Nucleic Acids Res. 1999. PMID: 9973633 Free PMC article.
• [Third-generation DNA sequencing: single molecule real-time DNA sequencing].
  Liu Y, Wu BQ. Liu Y, et al. Zhonghua Bing Li Xue Za Zhi. 2011 Oct;40(10):718-20. Zhonghua Bing Li Xue Za Zhi. 2011. PMID: 22321560 Review. Chinese. No abstract available.

Cited by

• MultiEditR: The first tool for the detection and quantification of RNA editing from Sanger sequencing demonstrates comparable fidelity to RNA-seq.
  Kluesner MG, Tasakis RN, Lerner T, Arnold A, Wüst S, Binder M, Webber BR, Moriarity BS, Pecori R. Kluesner MG, et al. Mol Ther Nucleic Acids. 2021 Jul 21;25:515-523. doi: 10.1016/j.omtn.2021.07.008. eCollection 2021 Sep 3. Mol Ther Nucleic Acids. 2021. PMID: 34589274 Free PMC article.
• Pairwise growth competition assay for determining the replication fitness of human immunodeficiency viruses.
  Manocheewa S, Lanxon-Cookson EC, Liu Y, Swain JV, McClure J, Rao U, Maust B, Deng W, Sunshine JE, Kim M, Rolland M, Mullins JI. Manocheewa S, et al. J Vis Exp. 2015 May 4;(99):e52610. doi: 10.3791/52610. J Vis Exp. 2015. PMID: 25993602 Free PMC article.
• Rapid detection of MYD88-L265P mutation by PCR-RFLP in B-cell lymphoproliferative disorders.
  Argentou N, Vassilopoulos G, Ioannou M, Germenis AE, Speletas M. Argentou N, et al. Leukemia. 2014 Feb;28(2):447-9. doi: 10.1038/leu.2013.294. Epub 2013 Oct 18. Leukemia. 2014. PMID: 24135828 No abstract available.
• A Guide to HIV-1 Reverse Transcriptase and Protease Sequencing for Drug Resistance Studies.
  Shafer RW, Dupnik K, Winters MA, Eshleman SH. Shafer RW, et al. HIV Seq Compend. 2001;2001:1-51. HIV Seq Compend. 2001. PMID: 22324021 Free PMC article. No abstract available.
• Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation.
  Garrick RC, Sunnucks P, Dyer RJ. Garrick RC, et al. BMC Evol Biol. 2010 Apr 30;10:118. doi: 10.1186/1471-2148-10-118. BMC Evol Biol. 2010. PMID: 20429950 Free PMC article.

Publication types

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Atypon
  • Taylor & Francis

• Other Literature Sources

  • The Lens - Patent Citations Database