A clustering method for repeat analysis in DNA sequences.
A clustering method for repeat analysis in DNA sequences.
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Date
2001-08-01
Authors
Volfovsky, Natalia
Haas, Brian J.
Salzberg, Steven L.
Advisor
Citation
A clustering method for repeat analysis in DNA sequences. N. Volfovsky, B.J. Haas, and S.L. Salzberg. Genome Biology 2:8 (2001), research0027:1-11.
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Abstract
Background: A computational system for analysis of the repetitive structure of genomic
sequences is described. The method uses suffix trees to organize and search the input sequences;
this data structure has been used previously for efficient computation of exact and degenerate
repeats.
Results: The resulting software tool collects all repeat classes and outputs summary statistics as
well as a file containing multiple sequences (multi fasta), that can be used as the target of searches.
Its use is demonstrated here on several complete microbial genomes, the entire Arabidopsis
thaliana genome, and a large collection of rice bacterial artificial chromosome end sequences.
Conclusions: We propose a new clustering method for analysis of the repeat data captured in suffix
trees. This method has been incorporated into a system that can find repeats in individual genome
sequences or sets of sequences, and that can organize those repeats into classes. It quickly and
accurately creates repeat databases from small and large genomes. The associated software
(RepeatFinder), should prove helpful in the analysis of repeat structure for both complete and partial
genome sequences.