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BMCBI
2005
84views more  BMCBI 2005»
14 years 9 months ago
Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates
Background: A new algorithm for assessing similarity between primer and template has been developed based on the hypothesis that annealing of primer to template is an information ...
Youfang Cao, Lianjie Wang, Kexue Xu, Chunhai Kou, ...
BMCBI
2002
108views more  BMCBI 2002»
14 years 9 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
ICML
2004
IEEE
15 years 3 months ago
Kernel-based discriminative learning algorithms for labeling sequences, trees, and graphs
We introduce a new perceptron-based discriminative learning algorithm for labeling structured data such as sequences, trees, and graphs. Since it is fully kernelized and uses poin...
Hisashi Kashima, Yuta Tsuboi
WABI
2004
Springer
15 years 3 months ago
Chaining Algorithms for Alignment of Draft Sequence
Abstract. In this paper we propose a chaining method that can align a draft genomic sequence against a finished genome. We introduce the use of an overlap tree to enhance the state...
Mukund Sundararajan, Michael Brudno, Kerrin Small,...
CPM
2005
Springer
206views Combinatorics» more  CPM 2005»
15 years 3 months ago
A Fast Algorithm for Approximate String Matching on Gene Sequences
Abstract. Approximate string matching is a fundamental and challenging problem in computer science, for which a fast algorithm is highly demanded in many applications including tex...
Zheng Liu, Xin Chen, James Borneman, Tao Jiang