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The Computer Journal Advance Access originally published online on June 27, 2007
The Computer Journal 2008 51(3):270-291; doi:10.1093/comjnl/bxm035
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© The Author 2007. Published by Oxford University Press on behalf of The British Computer Society. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Parameterized Complexity and Biopolymer Sequence Comparison

Liming Cai1,*, Xiuzhen Huang2, Chunmei Liu3, Frances Rosamond4,* and Yinglei Song5

1 Department of Computer Science, University of Georgia, Athens, GA 30605, USA
2 Department of Computer Science, Arkansas State University State University, AR, 72467, USA
3 Department of Systems and Computer Sciences, Howard University, Washington D.C. 20059, USA
4 Parameterized Complexity Research Unit, Auspices of the Office of DVC(Research), The University of Newcastle, Australia
5 Department of Mathematics and Computer Science, University of Maryland at Eastern Shore, Prince Anne, MD 21853, USA

* Corresponding author: cai{at}cs.uga.edu, mathgypsie{at}yahoo.com

Received 15 March 2006; revised 25 October 2006

The paper surveys parameterized algorithms and complexities for computational tasks on biopolymer sequences, including the problems of longest common subsequence, shortest common supersequence, pairwise sequence alignment, multiple sequencing alignment, structure–sequence alignment and structure–structure alignment. Algorithm techniques, built on the structural-unit level as well as on the residue level, are discussed.

Key Words: parameterized complexity • parameterized algorithms • pairwise sequence alignment • multiple sequence alignment • sequence–structure alignment • structure–structure alignment • tree width • tree decomposition • RNA secondary structure recognition and protein threading


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