Minimum common string partition revisited

Journal of Combinatorial Optimization

Volumn 23, Issue 4, 2012, Pages 519-527

  Jiang, Haitao ^a,b   Zhu, Binhai ^a   Zhu, Daming ^b   Zhu, Hong ^c  

^a Montana State University   (United States)

^b SHANDONG UNIVERSITY   (China)

^c EAST CHINA NORMAL UNIVERSITY   (China)

Author keywords

FPT algorithms; Genome rearrangement; Genomic distance; Minimum common string partition; NP completeness

Indexed keywords

FPT ALGORITHMS; GENOME REARRANGEMENTS; GENOMIC DISTANCE; MINIMUM COMMON STRING PARTITION; NP-COMPLETENESS;

COMPUTATIONAL COMPLEXITY; GENES;

APPROXIMATION ALGORITHMS;

EID: 84863726484     PISSN: 13826905     EISSN: 15732886     Source Type: Journal    
DOI: 10.1007/s10878-010-9370-2     Document Type: Article

References (15)

1. Chen X, Zheng J, Fu Z, Nan P, Zhong Y, Lonardi S, Jiang T (2005) Computing the assignment of orthologous genes via genome rearrangement. In: Proc of the 3rd Asia-Pacific bioinformatics conf (APBC'05), pp 363-378
2. Christie DA, Irving RW (2001) Sorting strings by reversals and by transpositions. SIAM J Discrete Math 14(2):193-206
3. Chrobak M, Kolman P, Sgall J (2004) The greedy algorithm for the minimum common string partition problem. In: Proc of the 7th international workshop on approximation algorithms for combinatorial optimization problems (APPROX'04). LNCS, vol 3122, pp 84-95
4. Cormode G, Muthukrishnan S (2002) The string edit distance matching problem with moves. In: Proc of the 13th ACM-SIAM symposium on discrete algorithms (SODA'02), pp 667-676
5. Damaschke P (2008) Minimum common string partition parameterized. In: Proc of the 8th workshop on algorithms in bioinformatics (WABI'08). LNCS, vol 5251, pp 87-98
6. Downey R, Fellows M (1999) Parameterized complexity. Springer, Berlin
7. Flum J, Grohe M (2006) Parameterized complexity theory. Springer, Berlin
8. Garey MR, Johnson DS (1979) Computers and intractability: A guide to the theory of NP-completeness. Freeman, New York
9. Goldstein A, Kolman P, Zheng J (2004) Minimum common string partitioning problem: Hardness and approximations. In: Proc of the 15th international symp on algorithms and computation (ISAAC'04). LNCS, vol 3341, pp 473-484. Also in: Electron J Comb 12, R50 (2005)
10. Jiang H, Zheng C, Sankoff D, Zhu B (2010) Scaffold filling under the breakpoint distance. In: Proc of the 8th annual RECOMB satellite workshop on comparative genomics (RECOMB-CG'10). LNBI, vol 6398, pp 83-92
11. Kaplan H, Shafrir N (2006) The greedy algorithm for edit distance with moves. Inf Process Lett 97(1):23-27
12. Kolman P (2005) Approximating reversal distance for strings with bounded number of duplicates. In: Proc of the 30th international symposium on mathematical foundations of computer science (MFCS'05). LNCS, vol 3618, pp 580-590
13. Kolman P, Walen T (2006) Reversal distance for strings with duplicates: Linear time approximation using hitting set. In: Proc 4th workshop on approximation and online algorithms (WAOA'06). LNCS, vol 4368, pp 279-289
14. Kolman P,Walen T (2007) Approximating reversal distance for strings with bounded number of duplicates. Discrete Appl Math 155(3):327-336
15. Shapira D, Storer J (2002) Edit distance with move operations. In: Proc of the 13th annual symposium on combinatorial pattern matching (CPM'02). LNCS, vol 2373, pp 85-98