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BMCBI
2004
130views more  BMCBI 2004»
13 years 6 months ago
PATTERNFINDER: combined analysis of DNA regulatory sequences and double-helix stability
Background: Regulatory regions that function in DNA replication and gene transcription contain specific sequences that bind proteins as well as less-specific sequences in which th...
Yanlin Huang, David Kowalski
EXPCS
2007
13 years 10 months ago
EXACT: the experimental algorithmics computational toolkit
In this paper, we introduce EXACT, the EXperimental Algorithmics Computational Toolkit. EXACT is a software framework for describing, controlling, and analyzing computer experimen...
William E. Hart, Jonathan W. Berry, Robert T. Heap...
CSB
2003
IEEE
108views Bioinformatics» more  CSB 2003»
14 years 10 hour ago
A Pattern Matching Algorithm for Codon Optimization and CpG Motif-Engineering in DNA Expression Vectors
Codon optimization enhances the efficiency of DNA expression vectors used in DNA vaccination and gene therapy by increasing protein expression. Additionally, certain nucleotide mo...
Ravi Vijaya Satya, Amar Mukherjee, Udaykumar Ranga
BMCBI
2008
132views more  BMCBI 2008»
13 years 6 months ago
The Average Mutual Information Profile as a Genomic Signature
Background: Occult organizational structures in DNA sequences may hold the key to understanding functional and evolutionary aspects of the DNA molecule. Such structures can also p...
Mark Bauer, Sheldon M. Schuster, Khalid Sayood
COMPLEX
2009
Springer
13 years 7 months ago
Moving Breather Collisions in the Peyrard-Bishop DNA Model
We consider collisions of moving breathers (MBs) in the Peyrard-Bishop DNA model. Two identical stationary breathers, separated by a fixed number of pair-bases, are perturbed and b...
A. Alvarez, F. R. Romero, J. Cuevas, J. F. R. Arch...