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» Revisiting the Sequence Constraint
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BMCBI
2002
108views more  BMCBI 2002»
15 years 6 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
HOTI
2008
IEEE
16 years 23 days ago
Constraint Repetition Inspection for Regular Expression on FPGA
— Recent network intrusion detection systems (NIDS) use regular expressions to represent suspicious or malicious character sequences in packet payloads in a more efficient way. ...
Miad Faezipour, Mehrdad Nourani
GIS
2008
ACM
16 years 7 months ago
The multi-rule partial sequenced route query
Trip planning search (TPS) represents an important class of queries in Geographic Information Systems (GIS). In many real-world applications, TPS requests are issued with a number...
Haiquan Chen, Wei-Shinn Ku, Min-Te Sun, Roger Zimm...
ICASSP
2007
IEEE
16 years 20 days ago
Evolutionary Sequence Modeling for Discovery of Peptide Hormones
There are currently a large number of ‘‘orphan’’ G-protein-coupled receptors (GPCRs) whose endogenous ligands (peptide hormones) are unknown. Identification of these pepti...
M. Kemal Sönmez, Lawrence Toll, Nina Zaveri
CPM
1993
Springer
154views Combinatorics» more  CPM 1993»
15 years 10 months ago
On Suboptimal Alignments of Biological Sequences
It is widely accepted that the optimal alignment between a pair of proteins or nucleic acid sequences that minimizes the edit distance may not necessarily re ect the correct biolog...
Dalit Naor, Douglas L. Brutlag