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BMCBI
2010

LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes

13 years 1 months ago
LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes
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). Results: To address these problems, we propose a novel approach that: (i)...
Zeev Frenkel, Etienne Paux, David I. Mester, Cathe
Added 28 Feb 2011
Updated 28 Feb 2011
Type Journal
Year 2010
Where BMCBI
Authors Zeev Frenkel, Etienne Paux, David I. Mester, Catherine Feuillet, Abraham B. Korol
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