title: Optimal spliced alignments of short sequence reads.
abstract: BACKGROUND
  Next generation sequencing technologies open exciting new possibilities for genome and transcriptome sequencing. While reads produced by these technologies are relatively short and error prone compared to the Sanger method their throughput is several magnitudes higher. To utilize such reads for transcriptome sequencing and gene structure identification, one needs to be able to accurately align the sequence reads over intron boundaries. This represents a significant challenge given their short length and inherent high error rate.
  
  
  RESULTS
  We present a novel approach, called QPALMA, 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. In computational experiments, we illustrate that the quality information as well as the splice site predictions help to improve the alignment quality. Finally, to facilitate mapping of massive amounts of sequencing data typically generated by the new technologies, we have combined our method with a fast mapping pipeline based on enhanced suffix arrays. Our algorithms were optimized and tested using reads produced with the Illumina Genome Analyzer for the model plant Arabidopsis thaliana.
  
  
  BACKGROUND
  Datasets for training and evaluation, additional results and a stand-alone alignment tool implemented in C++ and python are available at http://www.fml.mpg.de/raetsch/projects/qpalma.
authors.affiliation: Friedrich Miescher Laboratory, Max Planck Society, Spemannstr 39, 72076 Tübingen, Germany.
authors.forename: Fabio
authors.initials: F
authors.lastname: De Bona
authors.forename: Stephan
authors.initials: S
authors.lastname: Ossowski
authors.forename: Korbinian
authors.initials: K
authors.lastname: Schneeberger
authors.forename: Gunnar
authors.initials: G
authors.lastname: Rätsch
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D004274:DNA, Recombinant / Q000235:genetics*; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004274:DNA, Recombinant