Detection and correction of false segmental duplications caused by genome mis-assembly.
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.
Kelley
David R
DR
Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA. dakelley@umiacs.umd.edu
Salzberg
Steven L
SL
D000818:Animals; D001483:Base Sequence; D002417:Cattle; D002645:Chickens; D020451:Contig Mapping; D004171:Diploidy; D004285:Dogs; D023281:Genomics / Q000379:methods*; D006801:Humans; D002679:Pan troglodytes; D056916:Segmental Duplications, Genomic / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software