We describe a discriminatively trained sequence alignment model based on the averaged perceptron. In common with other approaches to sequence modeling using perceptrons, and in co...
Perceptron training is widely applied in the natural language processing community for learning complex structured models. Like all structured prediction learning frameworks, the ...
When aligning biological sequences, the choice of parameter values for the alignment scoring function is critical. Small changes in gap penalties, for example, can yield radically ...
Background: The sequencing of the human genome has enabled us to access a comprehensive list of genes (both experimental and predicted) for further analysis. While a majority of t...
Qicheng Ma, Gung-Wei Chirn, Richard Cai, Joseph D....
Background: High quality multiple alignments are crucial in the transfer of annotation from one genome to another. Multiple alignment methods strive to achieve ever increasing lev...