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» The Complexity of Phrase Alignment Problems
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127
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BMEI
2008
IEEE
15 years 9 months ago
A New Approach for Tree Alignment Based on Local Re-Optimization
Multiple sequence alignment is the most fundamental task in bioinformatics and computational biology. In this paper, we present a new algorithm to conduct multiple sequences align...
Feng Yue, Jijun Tang
138
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CPM
2008
Springer
154views Combinatorics» more  CPM 2008»
15 years 4 months ago
Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots
We present an algorithm for computing the edit distance of two RNA structures with arbitrary kinds of pseudoknots. A main benefit of the algorithm is that, despite the problem is N...
Mathias Möhl, Sebastian Will, Rolf Backofen
129
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CSJM
2006
59views more  CSJM 2006»
15 years 2 months ago
Traveling Salesman Problem with Transportation
Traveling Salesman Problem (TSP) is a generic name that includes diverse practical models. Motivated by applications, a new model of TSP is examined -- a synthesis of classical TS...
Valeriu Ungureanu
122
Voted
KELSI
2004
Springer
15 years 8 months ago
A Randomized Algorithm for Distance Matrix Calculations in Multiple Sequence Alignment
Multiple sequence alignment (MSA) is a vital problem in biology. Optimal alignment of multiple sequences becomes impractical even for a modest number of sequences [1] since the gen...
Sanguthevar Rajasekaran, Vishal Thapar, Hardik Dav...
114
Voted
BMCBI
2008
78views more  BMCBI 2008»
15 years 2 months ago
A new protein linear motif benchmark for multiple sequence alignment software
Background: Linear motifs (LMs) are abundant short regulatory sites used for modulating the functions of many eukaryotic proteins. They play important roles in post-translational ...
Emmanuel Perrodou, Claudia Chica, Olivier Poch, To...