Article

The greedy path-merging algorithm for sequence assembly

Authors:

Daniel H. Huson,

Knut Reinert,

Eugene MyersAuthors Info & Claims

RECOMB '01: Proceedings of the fifth annual international conference on Computational biology

Pages 157 - 163

https://doi.org/10.1145/369133.369190

Published: 22 April 2001 Publication History

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Abstract

Two different approaches to determining the human genome are currently being pursued: one is the “clone-by-clone” approach, employed by the publicly-funded. Human Genome Project, and the other is the “whole genome shotgun” approach, favored by researchers at Celera Genomics. An interim strategy employed at Celera, called hierarchical assembly, makes use of preliminary data produced by both approaches. This paper introduces the Bactig Ordering Problem, which is a key problem that arises in this context, and presents an efficient heuristic called the greedy path-merginq algorithm that performs well on real data.

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Cited By

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Ghurye JTreangen TFedarko MHervey WPop M(2019)MetaCarvel: linking assembly graph motifs to biological variantsGenome Biology10.1186/s13059-019-1791-320:1Online publication date: 26-Aug-2019
https://doi.org/10.1186/s13059-019-1791-3
Simpson JPop M(2015)The Theory and Practice of Genome Sequence AssemblyAnnual Review of Genomics and Human Genetics10.1146/annurev-genom-090314-05003216:1(153-172)Online publication date: 24-Aug-2015
https://doi.org/10.1146/annurev-genom-090314-050032
Koren STreangen TPop M(2011)Bambus 2Bioinformatics10.1093/bioinformatics/btr52027:21(2964-2971)Online publication date: 1-Nov-2011
https://dl.acm.org/doi/10.1093/bioinformatics/btr520
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Index Terms

The greedy path-merging algorithm for sequence assembly
1. Applied computing
  1. Life and medical sciences
2. Mathematics of computing
  1. Discrete mathematics

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Published In

RECOMB '01: Proceedings of the fifth annual international conference on Computational biology

April 2001

316 pages

ISBN:1581133537

DOI:10.1145/369133

Chairman:
Thomas Lengauer
German National Research Center for Information Technology, Germany

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 22 April 2001

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Conference

RECOMB01

Sponsor:

SIGACT

RECOMB01: The Fifth Annual International Conference on Computational Molecular Biology

April 22 - 25, 2001

Quebec, Montreal, Canada

Acceptance Rates

RECOMB '01 Paper Acceptance Rate 35 of 128 submissions, 27%;

Overall Acceptance Rate 148 of 538 submissions, 28%

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Cited By

View all

Ghurye JTreangen TFedarko MHervey WPop M(2019)MetaCarvel: linking assembly graph motifs to biological variantsGenome Biology10.1186/s13059-019-1791-320:1Online publication date: 26-Aug-2019
https://doi.org/10.1186/s13059-019-1791-3
Simpson JPop M(2015)The Theory and Practice of Genome Sequence AssemblyAnnual Review of Genomics and Human Genetics10.1146/annurev-genom-090314-05003216:1(153-172)Online publication date: 24-Aug-2015
https://doi.org/10.1146/annurev-genom-090314-050032
Koren STreangen TPop M(2011)Bambus 2Bioinformatics10.1093/bioinformatics/btr52027:21(2964-2971)Online publication date: 1-Nov-2011
https://dl.acm.org/doi/10.1093/bioinformatics/btr520
Nagarajan NPop M(2009)Parametric Complexity of Sequence Assembly: Theory and Applications to Next Generation SequencingJournal of Computational Biology10.1089/cmb.2009.000516:7(897-908)Online publication date: Jul-2009
https://doi.org/10.1089/cmb.2009.0005
Bartels DKespohl SAlbaum SDrüke TGoesmann AHerold JKaiser OPühler APfeiffer FRaddatz GStoye JMeyer FSchuster S(2005)BACCardI---a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparisonBioinformatics10.1093/bioinformatics/bti09121:7(853-859)Online publication date: 1-Apr-2005
https://dl.acm.org/doi/10.1093/bioinformatics/bti091
Pop MKosack DSalzberg S(2004)Hierarchical Scaffolding With BambusGenome Research10.1101/gr.153620414:1(149-159)Online publication date: 5-Jan-2004
https://doi.org/10.1101/gr.1536204
(2003)A Protein Sequence Prediction Method by Mining Sequence DataThe KIPS Transactions:PartD10.3745/KIPSTD.2003.10D.2.26110D:2(261-266)Online publication date: 1-Apr-2003
https://doi.org/10.3745/KIPSTD.2003.10D.2.261
Ben-Dor AKarp RSchwikowski BShamir R(2003)The Restriction Scaffold ProblemJournal of Computational Biology10.1089/1066527036068808410:3-4(385-398)Online publication date: Jun-2003
https://doi.org/10.1089/10665270360688084
Pop MSalzberg SShumway M(2002)Genome Sequence AssemblyComputer10.1109/MC.2002.101690135:7(47-54)Online publication date: 1-Jul-2002
https://dl.acm.org/doi/10.1109/MC.2002.1016901
Turner RChaturvedi KEdwards NFasulo DHalpern AHuson DKohlbacher OMiller JReinert KRemington KSchwartz RWalenz BYooseph SIstrail SBreen DHeirich AKoning A(2001)Visualization challenges for a new cyberpharmaceutical computing paradigmProceedings of the IEEE 2001 symposium on parallel and large-data visualization and graphics10.5555/502125.502127(7-18)Online publication date: 22-Oct-2001
https://dl.acm.org/doi/10.5555/502125.502127
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