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.

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.

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*