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» Alignment of Non-Overlapping Sequences
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111
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EMNLP
2007
15 years 4 months ago
A Sequence Alignment Model Based on the Averaged Perceptron
We describe a discriminatively trained sequence alignment model based on the averaged perceptron. In common with other approaches to sequence modeling using perceptrons, and in co...
Dayne Freitag, Shahram Khadivi
131
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JPDC
2006
112views more  JPDC 2006»
15 years 2 months ago
Large scale multiple sequence alignment with simultaneous phylogeny inference
Multiple sequence alignment (MSA) and phylogenetic tree reconstruction are one of the most important problems in the computational biology. While both these problems are of great ...
Gilles Parmentier, Denis Trystram, Jaroslaw Zola
123
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ISAAC
2004
Springer
114views Algorithms» more  ISAAC 2004»
15 years 8 months ago
Structural Alignment of Two RNA Sequences with Lagrangian Relaxation
RNA is generally a single-stranded molecule where the bases form hydrogen bonds within the same molecule leading to structure formation. In comparing different homologous RNA mole...
Markus Bauer, Gunnar W. Klau
129
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CIKM
2008
Springer
15 years 4 months ago
Pairwise statistical significance of local sequence alignment using multiple parameter sets
Background: Accurate estimation of statistical significance of a pairwise alignment is an important problem in sequence comparison. Recently, a comparative study of pairwise stati...
Ankit Agrawal, Xiaoqiu Huang
132
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JPDC
2007
167views more  JPDC 2007»
15 years 2 months ago
On the design of high-performance algorithms for aligning multiple protein sequences on mesh-based multiprocessor architectures
In this paper, we address the problem of multiple sequence alignment (MSA) for handling very large number of proteins sequences on mesh-based multiprocessor architectures. As the ...
Diana H. P. Low, Bharadwaj Veeravalli, David A. Ba...