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BMEI
2008
IEEE
14 years 2 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
IPPS
2009
IEEE
14 years 2 months ago
Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA
Computing large multiple protein sequence alignments using progressive alignment tools such as ClustalW requires several hours on state-of-the-art workstations. ClustalW uses a th...
Yongchao Liu, Bertil Schmidt, Douglas L. Maskell
COMPLIFE
2005
Springer
14 years 1 months ago
Fast and Accurate Structural RNA Alignment by Progressive Lagrangian Optimization
During the last few years new functionalities of RNA have been discovered, renewing the need for computational tools for their analysis. To this respect, multiple sequence alignmen...
Markus Bauer, Gunnar W. Klau, Knut Reinert
SSDBM
2006
IEEE
163views Database» more  SSDBM 2006»
14 years 1 months ago
ACache: Using Caching to Improve the Performance of Multiple Sequence Alignments
Multiple sequence alignment represents a class of powerful bioinformatics tools with many uses in computational biology ranging from discovery of characteristic motifs and conserv...
Xun Tu, Kajal T. Claypool, Cindy X. Chen
BMCBI
2006
117views more  BMCBI 2006»
13 years 7 months ago
Incorporating background frequency improves entropy-based residue conservation measures
Background: Several entropy-based methods have been developed for scoring sequence conservation in protein multiple sequence alignments. High scoring amino acid positions may corr...
Kai Wang, Ram Samudrala