RT Journal
A1 Bao, Zhirong
A1 Eddy, Sean R.
T1 Automated De Novo Identification of Repeat Sequence Families in Sequenced Genomes
JF Genome Research 
JO Genome Research 
YR 2002 
FD August 01 
VO 12 
IS 8 
SP 1269 
OP 1276 
DO 10.1101/gr.88502 
UL http://genome.cshlp.org/content/12/8/1269.abstract 
AB Repetitive sequences make up a major part of eukaryotic genomes. We have developed an approach for the de novo identification and classification of repeat sequence families that is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. Our extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. When tested on the human genome, our approach was able to properly identify and group known transposable elements. The program,RECON, should be useful for first-pass automatic classification of repeats in newly sequenced genomes.[The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: R. Klein.]