An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA. Export

@article{zhang:interval, abstract = {An algorithm is described for mapping DNA contigs based on an interval graph (IG) representation. In general terms, the input to the algorithm is a set of binary overlapping relations among finite intervals spread along a real line, from which the algorithm generates sets of ordered overlapping fragments spanning that line. The implications of a more general case of the IG, called a probe interval graph (PIG), in which only a subset of cosmids are used as probes, are also discussed. In the specific case of cosmids hybridizing to regions of a YAC, the algorithm takes cross-hybridization information using the cosmids as probes, and orders them along the YAC; if gaps exist due to insufficient coverage of cosmid contigs along the length of the YAC, repetitive use of the algorithm generates sets of ordered overlapping fragments. Both the IG and the PIG can expose problems caused by false overlaps, such as hybridizations due to repetitive elements. The algorithm, has been coded in C; CPU time is essentially linear with respect to the number of cosmids analyzed. Results are presented for the application of a PIG to cosmid contig assembly along a human chromosome 13-specific YAC. An alignment of 67 cosmids spanning a YAC took 0.28 seconds of CPU time on a Convex 220 computer.}, address = {Department of Genetics, Columbia University College of Physicians and Surgeons, New York, NY 10032.}, author = {Zhang, P. and Schon, E. A. and Fischer, S. G. and Cayanis, E. and Weiss, J. and Kistler, S. and Bourne, P. E.}, citeulike-article-id = {3196346}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/7922688}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=7922688}, issn = {0266-7061}, journal = {Computer applications in the biosciences : CABIOS}, keywords = {graph, interval, scaffolding, thesis}, month = {June}, number = {3}, pages = {309--317}, posted-at = {2008-09-04 22:40:45}, priority = {5}, title = {An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/7922688}, volume = {10}, year = {1994} }

TY - JOUR ID - zhang:interval L3 - citeulike-article-id:3196346 N2 - An algorithm is described for mapping DNA contigs based on an interval graph (IG) representation. In general terms, the input to the algorithm is a set of binary overlapping relations among finite intervals spread along a real line, from which the algorithm generates sets of ordered overlapping fragments spanning that line. The implications of a more general case of the IG, called a probe interval graph (PIG), in which only a subset of cosmids are used as probes, are also discussed. In the specific case of cosmids hybridizing to regions of a YAC, the algorithm takes cross-hybridization information using the cosmids as probes, and orders them along the YAC; if gaps exist due to insufficient coverage of cosmid contigs along the length of the YAC, repetitive use of the algorithm generates sets of ordered overlapping fragments. Both the IG and the PIG can expose problems caused by false overlaps, such as hybridizations due to repetitive elements. The algorithm, has been coded in C; CPU time is essentially linear with respect to the number of cosmids analyzed. Results are presented for the application of a PIG to cosmid contig assembly along a human chromosome 13-specific YAC. An alignment of 67 cosmids spanning a YAC took 0.28 seconds of CPU time on a Convex 220 computer. IS - 3 JF - Computer applications in the biosciences : CABIOS SN - 0266-7061 AD - Department of Genetics, Columbia University College of Physicians and Surgeons, New York, NY 10032. EP - 317 TI - An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA. VL - 10 SP - 309 KW - graph KW - interval KW - scaffolding KW - thesis AU - Zhang, P AU - Schon, EA AU - Fischer, SG AU - Cayanis, E AU - Weiss, J AU - Kistler, S AU - Bourne, PE PY - 1994/06// UR - http://view.ncbi.nlm.nih.gov/pubmed/7922688 ER -