LPmerge: an R package for merging genetic maps by linear programming

Consensus genetic maps constructed from multiple populations are an important resource for both basic and applied research, including genome-wide association analysis, genome sequence assembly and studies of evolution. The LPmerge software uses linear programming to efficiently minimize the mean abs...

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Veröffentlicht in:Bioinformatics Jg. 30; H. 11; S. 1623 - 1624
Hauptverfasser: Endelman, Jeffrey B., Plomion, Christophe
Format: Journal Article
Sprache:Englisch
Veröffentlicht: England Oxford University Press (OUP) 01.06.2014
Schlagworte:
Algorithms
Chromosome Mapping - methods
Genetic Linkage
Genetics
Life Sciences
Linear programming
Linkages
MAP (programming language)
Markers
Order disorder
Populations
Programming, Linear
Software
ISSN:1367-4803, 1367-4811, 1367-4811, 1460-2059
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Zusammenfassung:Consensus genetic maps constructed from multiple populations are an important resource for both basic and applied research, including genome-wide association analysis, genome sequence assembly and studies of evolution. The LPmerge software uses linear programming to efficiently minimize the mean absolute error between the consensus map and the linkage maps from each population. This minimization is performed subject to linear inequality constraints that ensure the ordering of the markers in the linkage maps is preserved. When marker order is inconsistent between linkage maps, a minimum set of ordinal constraints is deleted to resolve the conflicts. Availability and implementation: LPmerge is on CRAN at http://cran.r-project.org/web/packages/LPmerge. Contact:  endelman@wisc.edu Supplementary information:  Supplementary data are available at Bioinformatics online.
Bibliographie:ObjectType-Article-1
SourceType-Scholarly Journals-1
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content type line 23
ISSN:1367-4803
1367-4811
1367-4811
1460-2059
DOI:10.1093/bioinformatics/btu091