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

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


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Base Sequence
  • Cattle
  • Chickens
  • Contig Mapping
  • Diploidy*
  • Dogs
  • Genomics / methods*
  • Humans
  • Pan troglodytes
  • Segmental Duplications, Genomic / genetics*
  • Sequence Alignment
  • Sequence Analysis, DNA / methods*
  • Software*