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

• Published in: Genome biology Vol. 15; no. 2; p. R34
• Main Authors: Hoffmann, Steve, Otto, Christian, Doose, Gero, Tanzer, Andrea, Langenberger, David, Christ, Sabina, Kunz, Manfred, Holdt, Lesca M, Teupser, Daniel, Hackermüller, Jörg, Stadler, Peter F
• Format: Journal Article
• Language: English
• Published: England Springer-Verlag 10-02-2014; BioMed Central
• Subjects: Algorithms; complementary DNA; DNA, Complementary - genetics; gene fusion; High-Throughput Nucleotide Sequencing; messenger RNA; Method; nucleotide sequences; RNA - genetics; RNA Splicing - genetics; RNA, Circular; RNA, Messenger - metabolism; Software; Trans-Splicing - genetics
• ISSN: 1465-6906; 1474-760X; 1465-6914; 1474-760X
• DOI: 10.1186/gb-2014-15-2-r34

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/ ).