This article is part of the supplement: Highlights from the Fourth International Society for Computational Biology (ISCB) Student Council Symposium .

Oral presentation

Optimal spliced alignments of short sequence reads

Fabio De Bona¹ , Stephan Ossowski², Korbinian Schneeberger² and Gunnar Rätsch¹

¹  Friedrich Miescher Laboratory, Max Planck Society, Spemannstr. 39, 72076 Tübingen, Germany

²  Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076 Tübingen, Germany

author email corresponding author email

from Fourth International Society for Computational Biology (ISCB) Student Council Symposium
Toronto, Canada. 18 July 2008

BMC Bioinformatics 2008, 9(Suppl 10):O7doi:10.1186/1471-2105-9-S10-O7

Published:	30 October 2008

First paragraph (this article has no abstract)

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. We present a novel approach, called QPALMA, for computing accurate spliced alignments of short sequence reads that take advantage of the read's quality information as well as computational splice site predictions. In computational experiments we illustrate that the quality information as well as the splice site predictions [1] help to considerably improve the alignment quality. Our algorithms were optimized and tested using artificially spliced genomic reads produced with the Illumina Genome Analyzer for the model plant Arabidopsis thaliana.