Publications - Published papers

Please find below publications of our group. Currently, we list 508 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.

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

Steve Hoffmann, Christian Otto, Gero Doose, Andrea Tanzer, David Langenberger, Sabina Christ, Manfred Kunz, Lesca M. Holdt, Daniel Teupser, Jörg Hackermüller, Peter F. Stadler

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Genome Biology 2014, 15:R34

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 (www.bioinf.uni-leipzig.de/Software/segemehl/).

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