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BioMed Central, Genome Biology, 2(15), p. R34

DOI: 10.1186/gb-2014-15-2-r34

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A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

Journal article published in 2014 by Steve Hoffmann, Leipzig University Junior Research Group Transcriptome Bioinformatics, Christian Otto, Fakultat fur Chemie University of Vienna Institut fur Theoretische Chemie, Gero Doose, Andrea Tanzer ORCID, David Langenberger, Sabina Christ, Fraunhofer Institute for Cell Therapy and Immunology – IZI RNomics Group, Manfred Kunz, Venerology and Allergology Leipzig University Department of Dermatology, Lesca M. Holdt, Daniel Teupser, Leipzig University Life Research Center for Civilization Diseases, Jöerg Hackermüeller and other authors.
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Abstract Numerous high-throughput sequencing studies have focused on detecting conventionally spliced mRNAs in RNA-seq data. However, non-standard RNAs arising through gene fusion, circularization or trans-splicing are often neglected. We introduce a novel, unbiased algorithm to detect splice junctions from single-end cDNA sequences. In contrast to other methods, our approach accommodates multi-junction structures. Our method compares favorably with competing tools for conventionally spliced mRNAs and, with a gain of up to 40% of recall, systematically outperforms them on reads with multiple splits, trans-splicing and circular products. The algorithm is integrated into our mapping tool segemehl ( http://www.bioinf.uni-leipzig.de/Software/segemehl/ ).