Journal
GENOME RESEARCH
Volume 12, Issue 8, Pages 1269-1276Publisher
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gr.88502
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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.
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