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

Xiaoman Li | Zendy; Michael S. Waterman | Zendy

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

Author(s) -

Xiaoman Li,

Michael S. Waterman

Publication year - 2003

Publication title -

genome research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.556

H-Index - 297

eISSN - 1549-5469

pISSN - 1088-9051

DOI - 10.1101/gr.1251803

Subject(s) - shotgun sequencing , biology , genome , shotgun , hybrid genome assembly , k mer , tuple , computational biology , genetics , sequence assembly , dna sequencing , dna , gene , mathematics , discrete mathematics , gene expression , transcriptome

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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