Hoffmann Steve, Otto Christian, Doose Gero, Tanzer Andrea, Langenberger David, Christ Sabina, Kunz Manfred, Holdt Lesca M, Teupser Daniel, Hackermüller Jörg, Stadler Peter F
Genome Biol. 2014 Feb 10;15(2):R34. 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/).
众多高通量测序研究都聚焦于在RNA测序数据中检测常规剪接的mRNA。然而，由基因融合、环化或反式剪接产生的非标准RNA常常被忽视。我们引入了一种全新的、无偏差的算法，用于从单端cDNA序列中检测剪接接头。与其他方法不同，我们的方法能够处理多接头结构。在常规剪接的mRNA方面，我们的方法与其他竞争工具相比具有优势，并且在召回率上提高了多达40%，在具有多个片段、反式剪接和环状产物的 reads 上系统地优于它们。该算法已集成到我们的映射工具segemehl（http://www.bioinf.uni-leipzig.de/Software/segemehl/）中。
