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De novo repeat classification and fragment assembly.

ABSTRACT: 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.

SUBMITTER: Pevzner PA

PROVIDER: S-EPMC515325 | biostudies-literature | 2004 Sep

REPOSITORIES: biostudies-literature

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De novo repeat classification and fragment assembly.

Pevzner Pavel A PA Tang Haixu H Tesler Glenn G

Genome research 20040901 9

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 o ...[more]

PMID: 15342561

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