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» The Complexity of Phrase Alignment Problems
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BMEI
2008
IEEE
14 years 5 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
CPM
2008
Springer
154views Combinatorics» more  CPM 2008»
14 years 22 days 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
CSJM
2006
59views more  CSJM 2006»
13 years 11 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
KELSI
2004
Springer
14 years 4 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...
BMCBI
2008
78views more  BMCBI 2008»
13 years 11 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...