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» Constraint Based Methods for Biological Sequence Analysis
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BMCBI
2008
149views more  BMCBI 2008»
13 years 10 months ago
Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment s
Background: Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic d...
Olivier Bastien, Eric Maréchal
CSB
2002
IEEE
221views Bioinformatics» more  CSB 2002»
14 years 2 months ago
DNA Sequence Compression Using the Burrows-Wheeler Transform
-- We investigate off-line dictionary oriented approaches to DNA sequence compression, based on the Burrows-Wheeler Transform (BWT). The preponderance of short repeating patterns i...
Donald A. Adjeroh, Yong Zhang, Amar Mukherjee, Mat...
BMCBI
2010
116views more  BMCBI 2010»
13 years 10 months ago
SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments
Background: High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these ...
David B. Burdick, Christopher C. Cavnor, Jeremy Ha...
GECCO
2007
Springer
168views Optimization» more  GECCO 2007»
14 years 4 months ago
Sex and death: towards biologically inspired heuristics for constraint handling
Constrained continuous optimization is still an interesting field of research. Many heuristics have been proposed in the last decade. Most of them are based on penalty functions....
Oliver Kramer, Stephan Brügger, Dejan Lazovic
PAKDD
2004
ACM
183views Data Mining» more  PAKDD 2004»
14 years 3 months ago
Constraint-Based Graph Clustering through Node Sequencing and Partitioning
This paper proposes a two-step graph partitioning method to discover constrained clusters with an objective function that follows the well-known minmax clustering principle. Compar...
Yu Qian, Kang Zhang, Wei Lai