Sequencing two DNA templates in five channels by digital compression

Michael Nelson; Yanping Zhang; David L. Steffens; Reingard Grabherr; James L. Van Etten

doi:10.1073/pnas.90.5.1647

Sequencing two DNA templates in five channels by digital compression

Michael Nelson, Yanping Zhang, David L. Steffens, Reingard Grabherr, James L. Van Etten

Research output: Contribution to journal › Article › peer-review

9 Scopus citations

Abstract

By applying algebraic coding methods to the Sanger dideoxynucleotide procedure, DNA sequences of two templates can be determined simultaneously in only five reactions and data channels. A 5:2 data compression is accomplished by instantaneous source coding of nucleotide sequence pairs into one set of 5-bit block codes. A general algebraic expression, 2ⁿ - 1 ≥ 4^f, describes conditions under which f DNA templates can be sequenced using n channels. Such compression sequencing is accurate and efficient, as demonstrated by manual ³⁵S autoradiographic detection and automated on-line analysis using fluorescent-labeled primers. Symmetric 5:2 compression is especially useful when comparing two closely related sequences.

Original language	English (US)
Pages (from-to)	1647-1651
Number of pages	5
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	90
Issue number	5
DOIs	https://doi.org/10.1073/pnas.90.5.1647
State	Published - Mar 1 1993
Externally published	Yes

Keywords

Algebraic coding
Information theory

ASJC Scopus subject areas

General

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title = "Sequencing two DNA templates in five channels by digital compression",

abstract = "By applying algebraic coding methods to the Sanger dideoxynucleotide procedure, DNA sequences of two templates can be determined simultaneously in only five reactions and data channels. A 5:2 data compression is accomplished by instantaneous source coding of nucleotide sequence pairs into one set of 5-bit block codes. A general algebraic expression, 2n - 1 ≥ 4f, describes conditions under which f DNA templates can be sequenced using n channels. Such compression sequencing is accurate and efficient, as demonstrated by manual 35S autoradiographic detection and automated on-line analysis using fluorescent-labeled primers. Symmetric 5:2 compression is especially useful when comparing two closely related sequences.",

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AU - Zhang, Yanping

AU - Steffens, David L.

AU - Grabherr, Reingard

AU - Van Etten, James L.

PY - 1993/3/1

Y1 - 1993/3/1

N2 - By applying algebraic coding methods to the Sanger dideoxynucleotide procedure, DNA sequences of two templates can be determined simultaneously in only five reactions and data channels. A 5:2 data compression is accomplished by instantaneous source coding of nucleotide sequence pairs into one set of 5-bit block codes. A general algebraic expression, 2n - 1 ≥ 4f, describes conditions under which f DNA templates can be sequenced using n channels. Such compression sequencing is accurate and efficient, as demonstrated by manual 35S autoradiographic detection and automated on-line analysis using fluorescent-labeled primers. Symmetric 5:2 compression is especially useful when comparing two closely related sequences.

AB - By applying algebraic coding methods to the Sanger dideoxynucleotide procedure, DNA sequences of two templates can be determined simultaneously in only five reactions and data channels. A 5:2 data compression is accomplished by instantaneous source coding of nucleotide sequence pairs into one set of 5-bit block codes. A general algebraic expression, 2n - 1 ≥ 4f, describes conditions under which f DNA templates can be sequenced using n channels. Such compression sequencing is accurate and efficient, as demonstrated by manual 35S autoradiographic detection and automated on-line analysis using fluorescent-labeled primers. Symmetric 5:2 compression is especially useful when comparing two closely related sequences.

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Sequencing two DNA templates in five channels by digital compression

Abstract

Keywords

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