The steiner problem with edge lengths 1 and 2,
Information Processing Letters
Zinc finger gene clusters and tandem gene duplication
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
A More Efficient Approximation Scheme for Tree Alignment
SIAM Journal on Computing
Reconstructing the Duplication History of a Tandem Repeat
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
Efficient Methods for Inferring Tandem Duplication History
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Topological Rearrangements and Local Search Method for Tandem Duplication Trees
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Comparing Tandem Repeats with Duplications and Excisions of Variable Degree
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Improved Approximation Algorithms for Reconstructing the History of Tandem Repeats
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
An exact and polynomial distance-based algorithm to reconstruct single copy tandem duplication trees
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Alignment of tandem repeats with excision, duplication, substitution and indels (EDSI)
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Evolution of tandemly repeated sequences through duplication and inversion
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
Approximation algorithms for reconstructing the duplication history of tandem repeats
COCOON'07 Proceedings of the 13th annual international conference on Computing and Combinatorics
| Hi-index | 0.00 |
The genomes of many species are dominated by short sequences repeated consecutively called tandem repeats. An understanding of the biological mechanisms that create and extend tandem repeats would be facilitated by reconstructing the history of duplication events that generated the tandem repeats. This paper explores the computational problem of reconstructing the duplication history of a tandem repeat. Specifically, the problem of reconstructing the minimum-cost duplication history is proved to be NP-hard even if the lengths and boundaries for the duplication events are fixed. When the lengths and boundaries are fixed, the minimum-cost duplication history can actually be represented by a tree. A non-trivial extension of the tree-alignment algorithms from [Wang et al. (Algorithmica 16 (1996) 302; SIAM J. Comput. 30 (1) (2000) 283)] gives a polynomial time approximation scheme (PTAS) for this special case. Experiments on more than 9000 tandem repeats from human chromosomes 1 and 22 demonstrate that our PTAS generates less costly histories in acceptable time than other heuristic methods. We also note that our PTAS works for any metric space. Therefore, our algorithm is also a PTAS for constructing a minimum Steiner tree (MST) when the order of all the regular nodes on the output Steiner tree is known.Assigned to patriarchal poetry too sue sue sue sue shall sue sell and magnificent can as coming let the same shall shall shall shall let it share is share is share shall shall shall shall shell shell shall share is share shell can shell be shell be shell moving in in in inner moving move inner in in inner in meant meant might might may collect collected recollected to refuse what it is is it.