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BMCBI
2007
142views more  BMCBI 2007»
15 years 6 months ago
Improving model construction of profile HMMs for remote homology detection through structural alignment
Background: Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addre...
Juliana S. Bernardes, Alberto M. R. Dávila,...
BMCBI
2008
116views more  BMCBI 2008»
15 years 6 months ago
A novel representation of RNA secondary structure based on element-contact graphs
Background: Depending on their specific structures, noncoding RNAs (ncRNAs) play important roles in many biological processes. Interest in developing new topological indices based...
Wenjie Shu, Xiaochen Bo, Zhiqiang Zheng, Shengqi W...
BMCBI
2007
115views more  BMCBI 2007»
15 years 6 months ago
Correlation between structure and temperature in prokaryotic metabolic networks
Background: In recent years, an extensive characterization of network structures has been made in an effort to elucidate design principles of metabolic networks, providing valuabl...
Kazuhiro Takemoto, Jose C. Nacher, Tatsuya Akutsu
BMCBI
2011
15 years 1 months ago
Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars
Background: The prediction of the structure of large RNAs remains a particular challenge in bioinformatics, due to the computational complexity and low levels of accuracy of state...
Zsuzsanna Sukosd, Bjarne Knudsen, Morten Vaerum, J...
PLDI
2005
ACM
16 years 4 days ago
Automatic pool allocation: improving performance by controlling data structure layout in the heap
This paper describes Automatic Pool Allocation, a transformation framework that segregates distinct instances of heap-based data structures into seperate memory pools and allows h...
Chris Lattner, Vikram S. Adve