The deferred path heuristic for the generalized tree alignment problem

Author(s):  
Benno Schwikowski ◽  
Martin Vingron
1997 ◽  
Vol 4 (3) ◽  
pp. 415-431 ◽  
Author(s):  
BENNO SCHWIKOWSKI ◽  
MARTIN VINGRON

2017 ◽  
Author(s):  
Michela Quadrini ◽  
Luca Tesei ◽  
Emanuela Merelli ◽  

The methods proposed in the literature for RNA comparison focus mainly on pseudoknot free structures. The comparison of pseudoknotted structures is still a challenge. In this work, we propose a new algebraic representation of RNA secondary structures based on relations among hairpins in terms of nesting, crossing, and concatenation. Such algebraic representation is obtained from a defined multiple context-free grammar, which maps any kind of RNA secondary structures into extended trees, i.e., ordered trees where internal nodes are labeled with algebraic operators and leaves are labeled with loops. These extended trees permit the definition of the RNA secondary structure comparison as a tree alignment problem.


2017 ◽  
Author(s):  
Michela Quadrini ◽  
Luca Tesei ◽  
Emanuela Merelli ◽  

The methods proposed in the literature for RNA comparison focus mainly on pseudoknot free structures. The comparison of pseudoknotted structures is still a challenge. In this work, we propose a new algebraic representation of RNA secondary structures based on relations among hairpins in terms of nesting, crossing, and concatenation. Such algebraic representation is obtained from a defined multiple context-free grammar, which maps any kind of RNA secondary structures into extended trees, i.e., ordered trees where internal nodes are labeled with algebraic operators and leaves are labeled with loops. These extended trees permit the definition of the RNA secondary structure comparison as a tree alignment problem.


2012 ◽  
Vol 13 (1) ◽  
Author(s):  
Andrés Varón ◽  
Ward C Wheeler

Cladistics ◽  
2015 ◽  
Vol 32 (4) ◽  
pp. 452-460 ◽  
Author(s):  
Eric Ford ◽  
Ward C. Wheeler

Micromachines ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 673
Author(s):  
Wei Yuan ◽  
Cheng Xu ◽  
Li Xue ◽  
Hui Pang ◽  
Axiu Cao ◽  
...  

Double microlens arrays (MLAs) in series can be used to divide and superpose laser beam so as to achieve a homogenized spot. However, for laser beam homogenization with high coherence, the periodic lattice distribution in the homogenized spot will be generated due to the periodicity of the traditional MLA, which greatly reduces the uniformity of the homogenized spot. To solve this problem, a monolithic and highly integrated double-sided random microlens array (D-rMLA) is proposed for the purpose of achieving laser beam homogenization. The periodicity of the MLA is disturbed by the closely arranged microlens structures with random apertures. And the random speckle field is achieved to improve the uniformity of the homogenized spot by the superposition of the divided sub-beams. In addition, the double-sided exposure technique is proposed to prepare the rMLA on both sides of the same substrate with high precision alignment to form an integrated D-rMLA structure, which avoids the strict alignment problem in the installation process of traditional discrete MLAs. Then the laser beam homogenization experiments have been carried out by using the prepared D-rMLA structure. The laser beam homogenized spots of different wavelengths have been tested, including the wavelengths of 650 nm (R), 532 nm (G), and 405 nm (B). The experimental results show that the uniformity of the RGB homogenized spots is about 91%, 89%, and 90%. And the energy utilization rate is about 89%, 87%, 86%, respectively. Hence, the prepared structure has high laser beam homogenization ability and energy utilization rate, which is suitable for wide wavelength regime.


2009 ◽  
Vol 395 (1) ◽  
pp. 213-223 ◽  
Author(s):  
Erik Alm ◽  
Ralf J. O. Torgrip ◽  
K. Magnus Åberg ◽  
Ina Schuppe-Koistinen ◽  
Johan Lindberg

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