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» Sequence Database Search Using Jumping Alignments
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WABI
2009
Springer
128views Bioinformatics» more  WABI 2009»
15 years 9 months ago
A General Framework for Local Pairwise Alignment Statistics with Gaps
We present a novel dynamic programming framework that allows one to compute tight upper bounds for the p-values of gapped local alignments in pseudo–polynomial time. Our algorith...
Pasi Rastas
PAKDD
2007
ACM
115views Data Mining» more  PAKDD 2007»
15 years 9 months ago
Intelligent Sequential Mining Via Alignment: Optimization Techniques for Very Large DB
The shear volume of the results in traditional support based frequent sequential pattern mining methods has led to increasing interest in new intelligent mining methods to find mo...
Hye-Chung Kum, Joong Hyuk Chang, Wei Wang 0010
BMCBI
2008
108views more  BMCBI 2008»
15 years 3 months ago
A nonparametric model for quality control of database search results in shotgun proteomics
Background: Analysis of complex samples with tandem mass spectrometry (MS/MS) has become routine in proteomic research. However, validation of database search results creates a bo...
Jiyang Zhang, Jianqi Li, Xin Liu, Hongwei Xie, Yun...
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GECCO
2006
Springer
130views Optimization» more  GECCO 2006»
15 years 6 months ago
Pairwise sequence comparison for fitness evaluation in evolutionary structural software testing
Evolutionary algorithms are among the metaheuristic search methods that have been applied to the structural test data generation problem. Fitness evaluation methods play an import...
H. Turgut Uyar, A. Sima Etaner-Uyar, A. Emre Harma...
BMCBI
2010
135views more  BMCBI 2010»
15 years 3 months ago
A classification approach for genotyping viral sequences based on multidimensional scaling and linear discriminant analysis
Background: Accurate classification into genotypes is critical in understanding evolution of divergent viruses. Here we report a new approach, MuLDAS, which classifies a query seq...
Ji Woong Kim, Yongju Ahn, Kichan Lee, Sung-Hee Par...