An optimal procedure for gap closing in whole genome shotgun sequencing

R. Beigel; N. Alon; M. S. Apaydin; L. Fortnow; S. Kasif

doi:10.1145/369133.369152

An optimal procedure for gap closing in whole genome shotgun sequencing

R. Beigel
, N. Alon
, M. S. Apaydin
, L. Fortnow
, S. Kasif

Research output: Contribution to conference › Paper › peer-review

44 Scopus citations

Abstract

Tettelin et. al. proposed a new method for closing the gaps in whole genome shotgun sequencing projects. The method uses a multiplex PCR strategy in order to minimize the time and effort required to sequence the DNA in the missing gaps. This procedure has been used in a number of microbial sequencing projects including Streptococcus pneumoniae and other bacteria. In this paper we describe a theoretical framework for this problem and propose an improved method that guarantees to minimize the number of steps involved in the gap closure procedures. In particular, given a collection of n/2 DNA fragments we describe a strategy that requires 0.75n log n work in eight parallel rounds of experiments, closely matching a corresponding lower bound of 0.5n log n.

Original language	English
Pages	22-30
Number of pages	9
DOIs	https://doi.org/10.1145/369133.369152
State	Published - 1 Jan 2001
Externally published	Yes
Event	5th Annual Internatinal Conference on Computational Biology - Montreal, Que., Canada Duration: 22 May 2001 → 26 May 2001

Conference

Conference	5th Annual Internatinal Conference on Computational Biology
Country/Territory	Canada
City	Montreal, Que.
Period	22/05/01 → 26/05/01

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

ASJC Scopus subject areas

General Computer Science
General Biochemistry, Genetics and Molecular Biology

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10.1145/369133.369152

Cite this

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AU - Beigel, R.

AU - Alon, N.

AU - Apaydin, M. S.

AU - Fortnow, L.

AU - Kasif, S.

PY - 2001/1/1

Y1 - 2001/1/1

N2 - Tettelin et. al. proposed a new method for closing the gaps in whole genome shotgun sequencing projects. The method uses a multiplex PCR strategy in order to minimize the time and effort required to sequence the DNA in the missing gaps. This procedure has been used in a number of microbial sequencing projects including Streptococcus pneumoniae and other bacteria. In this paper we describe a theoretical framework for this problem and propose an improved method that guarantees to minimize the number of steps involved in the gap closure procedures. In particular, given a collection of n/2 DNA fragments we describe a strategy that requires 0.75n log n work in eight parallel rounds of experiments, closely matching a corresponding lower bound of 0.5n log n.

AB - Tettelin et. al. proposed a new method for closing the gaps in whole genome shotgun sequencing projects. The method uses a multiplex PCR strategy in order to minimize the time and effort required to sequence the DNA in the missing gaps. This procedure has been used in a number of microbial sequencing projects including Streptococcus pneumoniae and other bacteria. In this paper we describe a theoretical framework for this problem and propose an improved method that guarantees to minimize the number of steps involved in the gap closure procedures. In particular, given a collection of n/2 DNA fragments we describe a strategy that requires 0.75n log n work in eight parallel rounds of experiments, closely matching a corresponding lower bound of 0.5n log n.

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M3 - Paper

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T2 - 5th Annual Internatinal Conference on Computational Biology

Y2 - 22 May 2001 through 26 May 2001

ER -

An optimal procedure for gap closing in whole genome shotgun sequencing

Abstract

Conference

UN SDGs

ASJC Scopus subject areas

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