This Article Full Text Full Text (PDF) Supplemental Research Data Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Li, X. Articles by Waterman, M. S. Search for Related Content PubMed PubMed Citation Articles by Li, X. Articles by Waterman, M. S. Social Bookmarking                   What's this?

Methods

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

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

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 -tuple content of the reads.

³ Present address: Department of Statistics, Harvard University, Cambridge, MA 02138, USA.

⁴ Corresponding author. E-MAIL xiaomanl{at}yahoo.com; FAX (617) 496-8057.

[Supplemental material available online at www.genome.org.]

⁵ The left end of all reads consist of a homogeneous Poisson process with parameter c/L (Lander et al. 1988).

⁶ GroupNum is the maximal number of groups we used.

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				Y. Zhang and M. S. Waterman An Eulerian path approach to local multiple alignment for DNA sequences PNAS, February 1, 2005; 102(5): 1285 - 1290. [Abstract] [Full Text] [PDF]

				B. Raphael, D. Zhi, H. Tang, and P. Pevzner A novel method for multiple alignment of sequences with repeated and shuffled elements Genome Res., November 1, 2004; 14(11): 2336 - 2346. [Abstract] [Full Text] [PDF]

				P. A. Pevzner, H. Tang, and G. Tesler De Novo Repeat Classification and Fragment Assembly Genome Res., September 1, 2004; 14(9): 1786 - 1796. [Abstract] [Full Text] [PDF]

				R. DeMarco, A. T. Kowaltowski, A. A. Machado, M. B. Soares, C. Gargioni, T. Kawano, V. Rodrigues, A. M. B. N. Madeira, R. A. Wilson, C. F. M. Menck, et al. Saci-1, -2, and -3 and Perere, Four Novel Retrotransposons with High Transcriptional Activities from the Human Parasite Schistosoma mansoni J. Virol., March 15, 2004; 78(6): 2967 - 2978. [Abstract] [Full Text] [PDF]