An Eulerian path approach to DNA fragment assembly Export

@article{citeulike:79177, abstract = {10.1073/pnas.171285098 For the last 20 years, fragment assembly in DNA sequencing followed the \^{a}€œoverlap\^{a}€“layout\^{a}€“consensus\^{a}€ paradigm that is used in all currently available assembly tools. Although this approach proved useful in assembling clones, it faces difficulties in genomic shotgun assembly. We abandon the classical \^{a}€œoverlap\^{a}€“layout\^{a}€“consensus\^{a}€ approach in favor of a new algorithm that, for the first time, resolves the 20-year-old \^{a}€œrepeat problem\^{a}€ in fragment assembly. Our main result is the reduction of the fragment assembly to a variation of the classical Eulerian path problem that allows one to generate accurate solutions of large-scale sequencing problems. , in contrast to the assembler, does not mask such repeats but uses them instead as a powerful fragment assembly tool.}, address = {Department of Computer Science and Engineering, University of California, San Diego, La Jolla, USA.}, author = {Pevzner, Pavel A. and Tang, Haixu and Waterman, Michael S.}, citeulike-article-id = {79177}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.171285098}, citeulike-linkout-1 = {http://www.pnas.org/content/98/17/9748.abstract}, citeulike-linkout-2 = {http://www.pnas.org/content/98/17/9748.full.pdf}, citeulike-linkout-3 = {http://www.pnas.org/cgi/content/abstract/98/17/9748}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/11504945}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=11504945}, day = {14}, doi = {10.1073/pnas.171285098}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, keywords = {algorithms, assembly, sequencing}, month = {August}, number = {17}, pages = {9748--9753}, posted-at = {2009-11-07 19:10:27}, priority = {2}, title = {An Eulerian path approach to DNA fragment assembly}, url = {http://dx.doi.org/10.1073/pnas.171285098}, volume = {98}, year = {2001} }

TY - JOUR ID - citeulike:79177 L3 - citeulike-article-id:79177 N2 - 10.1073/pnas.171285098 For the last 20 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 useful in assembling clones, it faces difficulties in genomic shotgun assembly. We abandon the classical “overlap–layout–consensus” approach in favor of a new algorithm that, for the first time, resolves the 20-year-old “repeat problem” in fragment assembly. Our main result is the reduction of the fragment assembly to a variation of the classical Eulerian path problem that allows one to generate accurate solutions of large-scale sequencing problems. , in contrast to the assembler, does not mask such repeats but uses them instead as a powerful fragment assembly tool. IS - 17 JF - Proceedings of the National Academy of Sciences of the United States of America SN - 0027-8424 AD - Department of Computer Science and Engineering, University of California, San Diego, La Jolla, USA. EP - 9753 TI - An Eulerian path approach to DNA fragment assembly VL - 98 SP - 9748 KW - algorithms KW - assembly KW - sequencing AU - Pevzner, Pavel AU - Tang, Haixu AU - Waterman, Michael PY - 2001/08/14/ UR - http://dx.doi.org/10.1073/pnas.171285098 ER -