The Deferred Path Heuristic for the Generalized Tree Alignment Problem

1997 ◽  
Vol 4 (3) ◽  
pp. 415-431 ◽  
Author(s):  
BENNO SCHWIKOWSKI ◽  
MARTIN VINGRON
Keyword(s):  
Tree Alignment ◽  
Alignment Problem

scholarly journals An algebraic representation for tree alignment of RNA pseudoknotted structures

2017 ◽  
Author(s):  
Michela Quadrini ◽  
Luca Tesei ◽  
Emanuela Merelli ◽  
Keyword(s):  
Secondary Structures ◽  
Algebraic Representation ◽  
Structure Comparison ◽  
Rna Secondary Structures ◽  
Tree Alignment ◽  
Ordered Trees ◽  
Multiple Context ◽  
Alignment Problem ◽  
Definition Of ◽  
Context Free

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.

scholarly journals An algebraic representation for tree alignment of RNA pseudoknotted structures

2017 ◽  
Author(s):  
Michela Quadrini ◽  
Luca Tesei ◽  
Emanuela Merelli ◽  
Keyword(s):  
Secondary Structures ◽  
Algebraic Representation ◽  
Structure Comparison ◽  
Rna Secondary Structures ◽  
Tree Alignment ◽  
Ordered Trees ◽  
Multiple Context ◽  
Alignment Problem ◽  
Definition Of ◽  
Context Free

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.

scholarly journals The tree alignment problem

2012 ◽  
Vol 13 (1) ◽  
Author(s):  
Andrés Varón ◽  
Ward C Wheeler
Keyword(s):  
Tree Alignment ◽  
Alignment Problem

Comparison of heuristic approaches to the generalized tree alignment problem

Cladistics ◽  
2015 ◽  
Vol 32 (4) ◽  
pp. 452-460 ◽  
Author(s):  
Eric Ford ◽  
Ward C. Wheeler
Keyword(s):  
Tree Alignment ◽  
Heuristic Approaches ◽  
Alignment Problem

scholarly journals Integrated Double-Sided Random Microlens Array Used for Laser Beam Homogenization

Micromachines ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 673
Author(s):  
Wei Yuan ◽  
Cheng Xu ◽  
Li Xue ◽  
Hui Pang ◽  
Axiu Cao ◽  
...  
Keyword(s):  
Laser Beam ◽  
Microlens Array ◽  
Energy Utilization ◽  
Utilization Rate ◽  
Periodic Lattice ◽  
Lattice Distribution ◽  
Speckle Field ◽  
High Laser ◽  
Alignment Problem ◽  
In Series

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.

scholarly journals A solution to the 1D NMR alignment problem using an extended generalized fuzzy Hough transform and mode support

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