PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of narLink to Publisher's site
 
Nucleic Acids Res. 1995 April 25; 23(8): 1406–1410.
PMCID: PMC306869

The application of numerical estimates of base calling accuracy to DNA sequencing projects.

Abstract

During DNA sequencing projects one of the most labour intensive and highly skilled tasks is to view the original trace descriptions of gels and to adjudicate between conflicting readings. Given the current methods of calculating a consensus, the majority of the time employed in viewing traces and editing readings is actually devoted to making the poorer data fit the good data. We propose new consensus calculation algorithms that employ numerical estimates of base calling accuracy and which when used in conjunction with an automatic detector of contradictory data should greatly reduce the time spent checking and editing readings and hence improve DNA sequencing productivity.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (1.1M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Images in this article

Click on the image to see a larger version.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Dear S, Staden R. A sequence assembly and editing program for efficient management of large projects. Nucleic Acids Res. 1991 Jul 25;19(14):3907–3911. [PMC free article] [PubMed]
  • Gleeson T, Hillier L. A trace display and editing program for data from fluorescence based sequencing machines. Nucleic Acids Res. 1991 Dec 11;19(23):6481–6483. [PMC free article] [PubMed]
  • Smith S, Welch W, Jakimcius A, Dahlberg T, Preston E, Van Dyke D. High throughput DNA sequencing using an automated electrophoresis analysis system and a novel sequence assembly program. Biotechniques. 1993 Jun;14(6):1014–1018. [PubMed]
  • Lawrence CB, Solovyev VV. Assignment of position-specific error probability to primary DNA sequence data. Nucleic Acids Res. 1994 Apr 11;22(7):1272–1280. [PMC free article] [PubMed]
  • Lipshutz RJ, Taverner F, Hennessy K, Hartzell G, Davis R. DNA sequence confidence estimation. Genomics. 1994 Feb;19(3):417–424. [PubMed]
  • Dear S, Staden R. A standard file format for data from DNA sequencing instruments. DNA Seq. 1992;3(2):107–110. [PubMed]
  • Churchill GA, Waterman MS. The accuracy of DNA sequences: estimating sequence quality. Genomics. 1992 Sep;14(1):89–98. [PubMed]
  • Staden R. A new computer method for the storage and manipulation of DNA gel reading data. Nucleic Acids Res. 1980 Aug 25;8(16):3673–3694. [PMC free article] [PubMed]
  • Giddings MC, Brumley RL, Jr, Haker M, Smith LM. An adaptive, object oriented strategy for base calling in DNA sequence analysis. Nucleic Acids Res. 1993 Sep 25;21(19):4530–4540. [PMC free article] [PubMed]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press