TY - GEN
T1 - Aligning two fragmented sequences
AU - Veeramachaneni, V.
AU - Berman, P.
AU - Miller, W.
N1 - Funding Information:
This work was supported by grant HG02238 from the National Human Genome Research Institute.
Publisher Copyright:
© 2002 IEEE.
PY - 2002
Y1 - 2002
N2 - Upon completion of the human and mouse genome sequences, world-wide sequencing capacity will turn to other complex organisms. Current strategies call for many of these genomes to be incompletely sequenced. That is, holes will remain in the known sequence, and the relative order and orientation of the known sequence fragments may not be determined. Sequence comparison between two genomes of this sort may allow some of the fragments to be oriented and ordered relative to each other by computational means. We formalize this as an optimization problem, show that the problem is MAX-SNP hard, and develop a polynomial time algorithm that is guaranteed to produce a solution whose score is within a factor 3 of optimal.
AB - Upon completion of the human and mouse genome sequences, world-wide sequencing capacity will turn to other complex organisms. Current strategies call for many of these genomes to be incompletely sequenced. That is, holes will remain in the known sequence, and the relative order and orientation of the known sequence fragments may not be determined. Sequence comparison between two genomes of this sort may allow some of the fragments to be oriented and ordered relative to each other by computational means. We formalize this as an optimization problem, show that the problem is MAX-SNP hard, and develop a polynomial time algorithm that is guaranteed to produce a solution whose score is within a factor 3 of optimal.
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U2 - 10.1109/IPDPS.2002.1016591
DO - 10.1109/IPDPS.2002.1016591
M3 - Conference contribution
AN - SCOPUS:84966593234
T3 - Proceedings - International Parallel and Distributed Processing Symposium, IPDPS 2002
SP - 187
EP - 194
BT - Proceedings - International Parallel and Distributed Processing Symposium, IPDPS 2002
PB - Institute of Electrical and Electronics Engineers Inc.
T2 - 16th International Parallel and Distributed Processing Symposium, IPDPS 2002
Y2 - 15 April 2002 through 19 April 2002
ER -