QPALMA is a software for computing accurate spliced alignments which takes advantage of the read’s quality information as well as computational splice site predictions. Our method uses a training set of spliced reads with quality information and known alignments. It uses a large margin approach similar to support vector machines to estimate its parameters to maximize alignment accuracy.
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Bioinformatics. 2008 Aug 15;24(16):i174-80.
Optimal spliced alignments of short sequence reads.
De Bona F, Ossowski S, Schneeberger K, Rätsch G.