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» Fast Protein Structure Alignment
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ISMB
1997
13 years 9 months ago
Bayesian Adaptive Alignment and Inference
Sequencealignmentwithoutthe specification of gap penaltiesor a scoringmatrixis attainedbyusing Bayesianinferenceanda recursivealgorithm.Thisprocedure’srecursivealgorithmsumsover...
Jun Zhu, Jun S. Liu, Charles E. Lawrence
CIBCB
2005
IEEE
14 years 1 months ago
The Homology Kernel: A Biologically Motivated Sequence Embedding into Euclidean Space
— Part of the challenge of modeling protein sequences is their discrete nature. Many of the most powerful statistical and learning techniques are applicable to points in a Euclid...
Eleazar Eskin, Sagi Snir
NAR
2006
119views more  NAR 2006»
13 years 7 months ago
HHsenser: exhaustive transitive profile search using HMM-HMM comparison
HHsenser is the first server to offer exhaustive intermediate profile searches, which it combines with pairwise comparison of hidden Markov models. Starting from a single protein ...
Johannes Söding, Michael Remmert, Andreas Bie...
HPCC
2005
Springer
14 years 1 months ago
Fast Sparse Matrix-Vector Multiplication by Exploiting Variable Block Structure
Abstract. We improve the performance of sparse matrix-vector multiplication (SpMV) on modern cache-based superscalar machines when the matrix structure consists of multiple, irregu...
Richard W. Vuduc, Hyun-Jin Moon
CSB
2005
IEEE
114views Bioinformatics» more  CSB 2005»
14 years 1 months ago
Tree Decomposition Based Fast Search of RNA Structures Including Pseudoknots in Genomes
Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of effici...
Yinglei Song, Chunmei Liu, Russell L. Malmberg, Fa...