An algorithm for assembly of ordered restriction maps from single DNA molecules.

An algorithm for assembly of ordered restriction maps from single DNA molecules. Research Abstract Details 

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An algorithm for assembly of ordered restriction maps from single DNA molecules. Abstract Text:

Anton Valouev,David C Schwartz,Shiguo Zhou,Michael S Waterman,

The restriction mapping of a massive number of individual DNA molecules by optical mapping enables assembly of physical maps spanning mammalian and plant genomes; however, not through computational means permitting completely de novo assembly. Existing algorithms are not practical for genomes larger than lower eukaryotes due to their high time and space complexity. In many ways, sequence assembly parallels map assembly, so that the overlap-layout-consensus strategy, recently shown effective in assembling very large genomes in feasible time, sheds new light on solving map construction issues associated with single molecule substrates. Accordingly, we report an adaptation of this approach as the formal basis for de novo optical map assembly and demonstrate its computational feasibility for assembly of very large genomes. As such, we discuss assembly results for a series of genomes: human, plant, lower eukaryote and bacterial. Unlike sequence assembly, the optical map assembly problem is actually more complex because restriction maps from single molecules are constructed, manifesting errors stemming from: missing cuts, false cuts, and high variance of estimated fragment sizes; chimeric maps resulting from artifactually merged molecules; and true overlap scores that are "in the noise" or "slightly above the noise." We address these problems, fundamental to many single molecule measurements, by an effective error correction method using global overlap information to eliminate spurious overlaps and chimeric maps that are otherwise difficult to identify.

An algorithm for assembly of ordered restriction maps from single DNA molecules. Publishing Authors By Initials

A Valouev,DC Schwartz,S Zhou,MS Waterman,

For similar investigative techniques: genetic techniques: chromosome mapping: physical chromosome mapping: restriction mapping research abstracts see: investigative techniques: genetic techniques: chromosome mapping: physical chromosome mapping: restriction mapping research

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An algorithm for assembly of ordered restriction maps from single DNA molecules. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Proceedings of the National Academy of Sciences of

VOLUME: 103

Page Numbers: 15770-5

Journal Abbreviation: Proc. Natl. Acad. Sci. U.S.A.

ISSN: 0027-8424

DAY: 16

MONTH: 10

YEAR: 2006

An algorithm for assembly of ordered restriction maps from single DNA molecules. Information

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LANGUAGE: eng

NlmUniqueID: 7505876

An algorithm for assembly of ordered restriction maps from single DNA molecules. Keywords Mesh Terms:

KEYWORDS: Restriction Mapping

MESH TERMS: methods

Chemical & Substance for Abstract: An algorithm for assembly of ordered restriction maps from single DNA molecules. Information

Substance Name: DNA

Registry Number: 9007-49-2

Grant and Affiliation Information for An algorithm for assembly of ordered restriction maps from single DNA molecules.

AFFILIATION: Department of Mathematics, University of Southern California, 3620 South Vermont Avenue, KAP 108, Los Angeles, CA 90089-2532, USA. valouev@usc.edu

Country: United States

AGENCY: United States NHGRI

GRANT: P50 HG002790

ACRONYM: HG

MEDLINETA: Proc Natl Acad Sci U S A

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