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Genome Biol. 2010;11(3):R28. doi: 10.1186/gb-2010-11-3-r28. Epub 2010 Mar 10.

Detection and correction of false segmental duplications caused by genome mis-assembly.

Author information

1
Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA. dakelley@umiacs.umd.edu

Abstract

Diploid genomes with divergent chromosomes present special problems for assembly software as two copies of especially polymorphic regions may be mistakenly constructed, creating the appearance of a recent segmental duplication. We developed a method for identifying such false duplications and applied it to four vertebrate genomes. For each genome, we corrected mis-assemblies, improved estimates of the amount of duplicated sequence, and recovered polymorphisms between the sequenced chromosomes.

PMID:
20219098
PMCID:
PMC2864568
DOI:
10.1186/gb-2010-11-3-r28
[Indexed for MEDLINE]
Free PMC Article

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