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» Sequence Database Search Using Jumping Alignments
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NAR
2008
122views more  NAR 2008»
15 years 2 months ago
SIMAP - structuring the network of protein similarities
Protein sequences are the most important source of evolutionary and functional information for new proteins. In order to facilitate the computationally intensive tasks of sequence...
Thomas Rattei, Patrick Tischler, Roland Arnold, Fr...
228
Voted
SASP
2009
IEEE
291views Hardware» more  SASP 2009»
15 years 9 months ago
A parameterisable and scalable Smith-Waterman algorithm implementation on CUDA-compatible GPUs
—This paper describes a multi-threaded parallel design and implementation of the Smith-Waterman (SM) algorithm on compute unified device architecture (CUDA)-compatible graphic pr...
Cheng Ling, Khaled Benkrid, Tsuyoshi Hamada
150
Voted
ISCAPDCS
2007
15 years 4 months ago
Architectural requirements of parallel computational biology applications with explicit instruction level parallelism
—The tremendous growth in the information culture, efficient digital searches are needed to extract and identify information from huge data. The notion that evolution in silicon ...
Naeem Zafar Azeemi
115
Voted
BMCBI
2005
100views more  BMCBI 2005»
15 years 2 months ago
Evolutionary models for insertions and deletions in a probabilistic modeling framework
Background: Probabilistic models for sequence comparison (such as hidden Markov models and pair hidden Markov models for proteins and mRNAs, or their context-free grammar counterp...
Elena Rivas
121
Voted
BMCBI
2008
122views more  BMCBI 2008»
15 years 2 months ago
ESLpred2: improved method for predicting subcellular localization of eukaryotic proteins
Background: The expansion of raw protein sequence databases in the post genomic era and availability of fresh annotated sequences for major localizations particularly motivated us...
Aarti Garg, Gajendra P. S. Raghava