Estimating the Repeat Structure and Length of DNA Sequences Using  ℓ-Tuples

Xiaoman Li; Michael S. Waterman

doi:10.1101/gr.1251803

Methods

Estimating the Repeat Structure and Length of DNA Sequences Using ℓ-Tuples

- ¹ Department of Mathematics, University of Southern California, Los Angeles, California 90089, USA
- ² Celera Genomics, Rockville, Maryland 20850, USA

Published August 5, 2003. Vol 13 Issue 8, pp. 1916-1922. https://doi.org/10.1101/gr.1251803

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Abstract

In shotgun sequencing projects, the genome or BAC length is not always known. We approach estimating genome length by first estimating the repeat structure of the genome or BAC, sometimes of interest in its own right, on the basis of a set of random reads from a genome project. Moreover, we can find the consensus for repeat families before assembly. Our methods are based on the ℓ-tuple content of the reads.

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- Abstract
- RESULTS
- METHODS
- DISCUSSION
- Notes
- References