LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes |
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Authors: | Zeev Frenkel Etienne Paux David Mester Catherine Feuillet Abraham Korol |
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Institution: | 1.Institute of Evolution,University of Haifa,Haifa,Israel;2.INRA, Genetics,Diversity and Ecophysiology of Cereals,Clermont-Ferrand,France |
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Abstract: | Background Physical maps are the substrate of genome sequencing and map-based cloning and their construction relies on the accurate assembly
of BAC clones into large contigs that are then anchored to genetic maps with molecular markers. High Information Content Fingerprinting
has become the method of choice for large and repetitive genomes such as those of maize, barley, and wheat. However, the high
level of repeated DNA present in these genomes requires the application of very stringent criteria to ensure a reliable assembly
with the FingerPrinted Contig (FPC) software, which often results in short contig lengths (of 3-5 clones before merging) as
well as an unreliable assembly in some difficult regions. Difficulties can originate from a non-linear topological structure
of clone overlaps, low power of clone ordering algorithms, and the absence of tools to identify sources of gaps in Minimal
Tiling Paths (MTPs). |
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Keywords: | |
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