Embedding planar graphs in four pages
Journal of Computer and System Sciences - 18th Annual ACM Symposium on Theory of Computing (STOC), May 28-30, 1986
Graphs with small bandwidth and cutwidth
Discrete Mathematics
Tree-width, path-width, and cutwidth
Discrete Applied Mathematics
The longest common subsequence problem for sequences with nested arc annotations
Journal of Computer and System Sciences - Computational biology 2002
On the Complexity of Protein Similarity Search under mRNA Structure Constraints
STACS '02 Proceedings of the 19th Annual Symposium on Theoretical Aspects of Computer Science
Parameterized Complexity
Polynomial algorithms for protein similarity search for restricted mRNA structures
Information Processing Letters
Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Cutwidth of Split Graphs, Threshold Graphs, and Proper Interval Graphs
Graph-Theoretic Concepts in Computer Science
Computing the cutwidth of bipartite permutation graphs in linear time
WG'10 Proceedings of the 36th international conference on Graph-theoretic concepts in computer science
A branch-and-bound algorithm for the minimum cut linear arrangement problem
Journal of Combinatorial Optimization
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In the context of protein engineering, we consider the problem of computing an mRnA sequence of maximal codon-wise similarity to a given mRnA (and consequently, to a given protein) that additionally satisfies some secondary structure constraints, the so-called MRSO problem [2]. Since the MRSO problem is known to be APX-hard [8], Bongartz proposed in [8] to attack the problem using the concept of parameterized complexity. In this paper we follow this suggested approach by devising fixed-parameter algorithms for several interesting parameters of MRSO. We believe these algorithms to be relevant for practical applications today, as well as for several future applications. Furthermore, our results extend the known tractability borderline of MRSO, and provide new research horizons for further improvements of this sort.