A new approach to fragment assembly in DNA sequencing

For the last twenty years fragment assembly in DNA sequencing followed the "overlap - layout - consensus" paradigm that is used in all currently available assembly tools. Although this approach proved to be useful in assembling clones, it faces difficulties in genomic shotgun assembly: the existing algorithms make assembly errors and are often unable to resolve repeats even in prokaryotic genomes. Biologists are well-aware of these errors and are forced to carry additional experiments to verify the assembled contigs. We abandon the classical "overlap - layout - consensus" approach in favor of a new Eulerian Superpath approach that, for the first time, resolves the problem of repeats in fragment assembly. Our main result is the reduction of the fragment assembly to a variation of the classical Eulerian path problem. This reduction opens new possibilities for repeat resolution and allows one to generate error-free solutions of the large-scale fragment assembly proble...

• Type: Conference
• Year: 2001
• Where: RECOMB
• Authors: Pavel A. Pevzner, Haixu Tang, Michael S. Waterman
• Keywords: Classical Eulerian Path, Computational Biology, Fragment Assembly, Long Perfect Repeats, RECOMB 2001