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» Alignment of Non-Overlapping Sequences
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86
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DKE
2008
91views more  DKE 2008»
15 years 22 days ago
SUSAX: Context-specific searching in XML documents using sequence alignment techniques
Keyword searching while very successful in narrowing down the contents of the Web to the pertaining subset of information, has two primary drawbacks. First, the accuracy of the se...
Kajal T. Claypool
102
Voted
ALMOB
2008
85views more  ALMOB 2008»
15 years 24 days ago
Noisy: Identification of problematic columns in multiple sequence alignments
Motivation: Sequence-based methods for phylogenetic reconstruction from (nucleic acid) sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Larg...
Andreas W. M. Dress, Christoph Flamm, Guido Fritzs...
90
Voted
AAAI
2000
15 years 2 months ago
Divide-and-Conquer Frontier Search Applied to Optimal Sequence Alignment
We present a new algorithm that reduces the space complexity of heuristic search. It is most effective for problem spaces that grow polynomially with problem size, but contain lar...
Richard E. Korf, Weixiong Zhang
IJBRA
2006
111views more  IJBRA 2006»
15 years 19 days ago
Memory efficient alignment between RNA sequences and stochastic grammar models of pseudoknots
: Stochastic Context-Free Grammars (SCFG) has been shown to be effective in modelling RNA secondary structure for searches. Our previous work (Cai et al., 2003) in Stochastic Paral...
Yinglei Song, Chunmei Liu, Russell L. Malmberg, Co...
121
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BMCBI
2008
211views more  BMCBI 2008»
15 years 23 days ago
CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment
Background: Searching for similarities in protein and DNA databases has become a routine procedure in Molecular Biology. The Smith-Waterman algorithm has been available for more t...
Svetlin Manavski, Giorgio Valle