title: FUSIM: a software tool for simulating fusion transcripts.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  FUSIM provides the ability to assemble a dataset of fusion transcripts useful for testing and benchmarking applications in fusion gene discovery.
authors: Department of Biostatistics, SUNY at Buffalo, Buffalo, NY 14214, USA. aebruno2@buffalo.edu
authors: Andrew E
authors: AE
authors: Bruno
authors: Jeffrey C
authors: JC
authors: Miecznikowski
authors: Maochun
authors: M
authors: Qin
authors: Jianmin
authors: J
authors: Wang
authors: Song
authors: S
authors: Liu
mesh_terms: D003198:Computer Simulation; D020869:Gene Expression Profiling; D050939:Gene Fusion; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D050506:Mutant Chimeric Proteins / Q000235:genetics; D012313:RNA / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D050506:Mutant Chimeric Proteins; D012313:RNA