We propose a sequence-alignment based method for detecting and disambiguating coordinate conjunctions. In this method, averaged perceptron learning is used to adapt the substituti...
Background: Multiple sequence alignment is fundamental. Exponential growth in computation time appears to be inevitable when an optimal alignment is required for many sequences. E...
Background: Accurate sequence alignments are essential for homology searches and for building three-dimensional structural models of proteins. Since structure is better conserved ...
Accurately aligning distant protein sequences is notoriously difficult. A recent approach to improving alignment accuracy is to use additional information such as predicted seconda...
When aligning biological sequences, the choice of scoring scheme is critical. Even small changes in gap penalties, for example, can yield radically different alignments. A rigorous...