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Open Access Software

FUSIM: a software tool for simulating fusion transcripts

Andrew E Bruno123*, Jeffrey C Miecznikowski12, Maochun Qin2, Jianmin Wang12* and Song Liu12*

Author Affiliations

1 Department of Biostatistics, SUNY at Buffalo, , Buffalo, NY 14214, USA

2 Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA

3 Center for Computational Research, SUNY at Buffalo, , Buffalo, NY, 14260, USA

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BMC Bioinformatics 2013, 14:13  doi:10.1186/1471-2105-14-13

Published: 16 January 2013



Gene fusions are the result of chromosomal aberrations and encode chimeric RNA (fusion transcripts) that play an important role in cancer genesis. Recent advances in high throughput transcriptome sequencing have given rise to computational methods for new fusion discovery. The ability to simulate fusion transcripts is essential for testing and improving those tools.


To facilitate this need, we developed FUSIM (FUsion SIMulator), a software tool for simulating fusion transcripts. The simulation of events known to create fusion genes and their resulting chimeric proteins is supported, including inter-chromosome translocation, trans-splicing, complex chromosomal rearrangements, and transcriptional read through events.


FUSIM provides the ability to assemble a dataset of fusion transcripts useful for testing and benchmarking applications in fusion gene discovery.