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» New Algorithms for SIMD Alignment
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BMCBI
2010
90views more  BMCBI 2010»
13 years 8 months ago
Local alignment of generalized k-base encoded DNA sequence
Background: DNA sequence comparison is a well-studied problem, in which two DNA sequences are compared using a weighted edit distance. Recent DNA sequencing technologies however o...
Nils Homer, Stanley F. Nelson, Barry Merriman
IPPS
2002
IEEE
14 years 22 days ago
Massively Parallel Solutions for Molecular Sequence Analysis
In this paper we present new approaches to high performance protein database scanning on two novel massively parallel architectures to gain supercomputer power at low cost. The ï¬...
Bertil Schmidt, Heiko Schröder, Manfred Schim...
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
WOB
2004
120views Bioinformatics» more  WOB 2004»
13 years 9 months ago
Reconfigurable Systems for Sequence Alignment and for General Dynamic Programming
ABSTRACT. Reconfigurable systolic arrays can be adapted to efficiently resolve a wide spectrum of computational problems; parallelism is naturally explored in systolic arrays and r...
Ricardo P. Jacobi, Mauricio Ayala-Rincón, L...
CVPR
2009
IEEE
15 years 2 months ago
On Compositional Image Alignment with an Application to Active Appearance Models
Efficient and accurate fitting of Active Appearance Models (AAM) is a key requirement for many applications. The most efficient fitting algorithm today is Inverse Compositional ...
Brian Amberg (University of Basel), Andrew Blake (...