Work

De Novo Repeat Classification and Fragment Assembly

Year: 2004

Type: preprint

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.

Source: Genome Research

DOI: 10.1101/gr.2395204

Authors: Paul A. Pevzner, Haixu Tang, Glenn Tesler

Institution: University of California San Diego

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: bronze

Funder: National Human Genome Research Institute

Award: A New Approach to Fragment Assembly in DNA Sequencing