NDLI: Colored de Bruijn Graphs and the Genome Halving Problem

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Colored de Bruijn Graphs and the Genome Halving Problem

Content Provider	ACM Digital Library
Author	Pevzner, Pavel A. Alekseyev, Max A.
Abstract	Breakpoint graph analysis is a key algorithmic technique in studies of genome rearrangements. However, breakpoint graphs are defined only for genomes without duplicated genes, thus limiting their applications in rearrangement analysis. We discuss a connection between the breakpoint graphs and de Bruijn graphs that leads to a generalization of the notion of breakpoint graph for genomes with duplicated genes. We further use the generalized breakpoint graphs to study the Genome Halving Problem (first introduced and solved by Nadia El-Mabrouk and David Sankoff). The El-Mabrouk-Sankoff algorithm is rather complex, and, in this paper, we present an alternative approach that is based on generalized breakpoint graphs. The generalized breakpoint graphs make the El-Mabrouk-Sankoff result more transparent and promise to be useful in future studies of genome rearrangements.
Starting Page	98
Ending Page	107
Page Count	10
File Format	PDF
ISSN	15455963
DOI	10.1109/TCBB.2007.1002
Volume Number	4
Issue Number	1
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2007-01-01
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Genome duplication, genome halving, genome rearrangement, reversal, breakpoint graph, de Bruijn graph.
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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Colored de Bruijn Graphs and the Genome Halving Problem

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© by the Institute of Electrical and Electronics Engineers (IEEE) Colored de Bruijn Graphs and the Genome Halving Problem

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