Skip Navigation

This Article
Right arrow Print PDF (809K)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (19)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Lawrence, C. B.
Right arrow Articles by Solovyev, V. V.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Lawrence, C. B.
Right arrow Articles by Solovyev, V. V.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 1994, Vol. 22, No. 7 1272-1280
© 1994

GENOME STRUCTURE AND MAPPING

Assignment of position-specific error probability to primary DNA sequence data

Charles B. Lawrence* and Victor V. Solovyev

Department of Cell Biology, Baylor College of Medicine, One Baylor Plaza Houston, TX 77030, USA

*To whom correspondence should be addressed

Received October 27, 1993. Revised February 24, 1994. Accepted February 24, 1994.

DNA sequence predicted from polyacrylamide gel-based technologies is inaccurate because of variations in the quality of the primary data due to limitations of the technology, and to sequence-specific variations due to nucleotide interactions within the DNA molecule and with the gel. The ability to recognize the probability of error in the primary data will be useful in reconstructing the target sequence of a DNA sequencing project, and in estimating the accuracy of the final sequence. This paper describes the use of linear discriminant analysis to assign position-specific probabilities of incorrect, over- and under- prediction of nucleotides for each predicted nucleotide position in primary sequence data generated by a gel-based DNA sequencing technology. Using this method, most of the error potential in primary sequence data can be assigned to a limited number of discrete positions. The use of probability values in the sequence reconstruction process, and in estimating the accuracy of consensus sequence determination is described.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Proc. Natl. Acad. Sci. USAHome page
R. G. Eason, N. Pourmand, W. Tongprasit, Z. S. Herman, K. Anthony, O. Jejelowo, R. W. Davis, and V. Stolc
Characterization of synthetic DNA bar codes in Saccharomyces cerevisiae gene-deletion strains
PNAS, July 27, 2004; 101(30): 11046 - 11051.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
D. Walther, G. Bartha, and M. Morris
Basecalling with LifeTrace
Genome Res., May 1, 2001; 11(5): 875 - 888.
[Abstract] [Full Text]

Home page
 Genome ResHome page
R. Durbin and S. Dear
Base Qualities Help Sequencing Software
Genome Res., March 1, 1998; 8(3): 161 - 162.
[Full Text]

Home page
 Genome ResHome page
B. Ewing and P. Green
Base-Calling of Automated Sequencer Traces Using Phred.  II. Error Probabilities
Genome Res., March 1, 1998; 8(3): 186 - 194.
[Abstract] [Full Text]

Home page
 Genome ResHome page
P. Richterich
Estimation of Errors in "Raw" DNA Sequences: A Validation Study
Genome Res., March 1, 1998; 8(3): 251 - 259.
[Abstract] [Full Text]

Home page
 Genome ResHome page
J. L. Weber and E. W. Myers
Human Whole-Genome Shotgun Sequencing
Genome Res., May 1, 1997; 7(5): 401 - 409.
[Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.