EULERIAN PATH APPROACH TO DNA FRAGMENT ASSEMBLY

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Euler is a new approach to fragment assembly that abandons the classical "overlap - layout - consensus" paradigm that is used in all currently available assembly tools. See EULER papers for details. 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 shortcomings and are often unable to resolve repeats even in prokaryotic genomes. Biologists are well-aware of these errors and are forced to carry out additional experiments to verify the assembled contigs. We abandon the classical "overlap - layout - consensus" approach in favor of a new Eulerian Superpath approach. EULER, in contrast to the Celera assembler, does not mask repeats but uses them instead as a powerful fragment assembly tool. This EULER server provides an online tool to assemble DNA sequences.