Work

Automated De Novo Identification of Repeat Sequence Families in Sequenced Genomes

Year: 2002

Type: preprint

Abstract: 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, should be useful for first-pass automatic classification of repeats in newly sequenced genomes.

Source: Genome Research

DOI: 10.1101/gr.88502

Authors: Zhirong Bao, Sean R. Eddy

Institutions: Howard Hughes Medical Institute, Washington University in St. Louis

Language: English

Topic: Chromosomal and Genetic Variations

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: bronze

Funders: National Science Foundation, Howard Hughes Medical Institute

Award: Transposable Elements in Rice: A Whole Genome Approach