De novo repeat classification and fragment assembly

Pavel A. Pevzner, Haixu Tang, Glenn Tesler
2004 Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04  
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.
doi:10.1145/974614.974643 dblp:conf/recomb/PevznerTT04 fatcat:wfgtq6ypinf6npzynot7lzc464