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BMCBI
2008
105views more  BMCBI 2008»
15 years 4 months ago
A gene pattern mining algorithm using interchangeable gene sets for prokaryotes
Background: Mining gene patterns that are common to multiple genomes is an important biological problem, which can lead us to novel biological insights. When family classification...
Meng Hu, Kwangmin Choi, Wei Su, Sun Kim, Jiong Yan...
MAM
2007
157views more  MAM 2007»
15 years 4 months ago
Executing large algorithms on low-capacity FPGAs using flowpath partitioning and runtime reconfiguration
This paper describes a new method of executing a software program on an FPGA for embedded systems. Rather than combine reconfigurable logic with a microprocessor core, this method...
Darrin M. Hanna, Michael DuChene
BMCBI
2002
108views more  BMCBI 2002»
15 years 4 months ago
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure
Background: Covariance models (CMs) are probabilistic models of RNA secondary structure, analogous to profile hidden Markov models of linear sequence. The dynamic programming algo...
Sean R. Eddy
BMCBI
2011
14 years 8 months ago
Protein alignment algorithms with an efficient backtracking routine on multiple GPUs
Background: Pairwise sequence alignment methods are widely used in biological research. The increasing number of sequences is perceived as one of the upcoming challenges for seque...
Jacek Blazewicz, Wojciech Frohmberg, Michal Kierzy...
ESA
2001
Springer
105views Algorithms» more  ESA 2001»
15 years 9 months ago
SNPs Problems, Complexity, and Algorithms
Abstract. Single nucleotide polymorphisms (SNPs) are the most frequent form of human genetic variation. They are of fundamental importance for a variety of applications including m...
Giuseppe Lancia, Vineet Bafna, Sorin Istrail, Ross...