De novo repeat classification and fragment assembly

Repetitive sequences make up a significant fraction of almost any genome, and an important and still open question in bioinformatics is how to represent all repeats in DNA sequences. We propose a new approach to repeat classification that represents all repeats in a genome as a mosaic of sub-repeats...

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Bibliographic Details
Published inGenome research Vol. 14; no. 9; pp. 1786 - 1796
Main Authors Pevzner, Pavel A, Pevzner, Paul A, Tang, Haixu, Tesler, Glenn
Format Journal Article
LanguageEnglish
Published United States Cold Spring Harbor Laboratory Press 01.09.2004
Subjects
Algorithms
Chromosomes, Artificial, Bacterial
Cluster Analysis
Computational Biology - methods
Computational Biology - statistics & numerical data
Contig Mapping - methods
Genetic Linkage - genetics
Genome, Human
Humans
Methods
Multigene Family - genetics
Repetitive Sequences, Nucleic Acid - genetics
Sequence Alignment - methods
Sequence Alignment - statistics & numerical data
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Summary:Repetitive sequences make up a significant fraction of almost any genome, and an important and still open question in bioinformatics is how to represent all repeats in DNA sequences. We propose a new approach to repeat classification that represents all repeats in a genome as a mosaic of sub-repeats. Our key algorithmic idea also leads to new approaches to multiple alignment and fragment assembly. In particular, we show that our FragmentGluer assembler improves on Phrap and ARACHNE in assembly of BACs and bacterial genomes.
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Corresponding author. E-MAIL gptesler@math.ucsd.edu ; FAX (858) 534-7029.
ISSN:1088-9051
DOI:10.1101/gr.2395204