Department of Bioinformatics and Computational Biology


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BreakTrans: uncover the genomic architecture of gene fusions
Description BreakTrans maps gene fusions to genomic architecture in cancer cells
Development Information
Language Perl
Current Version 0.0.6
License GPL v3
Status Active
Last Updated 2013/02/13
Citations Chen K, Navin NE, Wang Y, Schmidt HK, Wallis JW, Niu B, Fan X, Zhao H, McLellan MD, Hoadley KA, Mardis ER, Ley TJ, Perou CM, Wilson RK, Ding L. BreakTrans: uncovering the genomic architecture of gene fusions. Genome Biol 14(8). e-Pub 8/2013. PMID: 23972288
News N.A.
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Contact Ken Chen
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BreakTrans is a computer program that maps predicted gene fusions to genomic structural rearrangements so as to validate both types of events and provide them mechanism/functional interpretation. It requires input from at least one gene fusion prediction program (such as Tophat-fusion, deFuse and BreakFusion) and at least one genomic breakpoint detection program (such as BreakDancer and CREST).



The BreakTrans package includes two parts, executable files and annotation data files for each specific cancer. To run it, users need to download the executable files and the annotation database.
Executable Package (6.5 Kb)
* BreakTrans-0.0.6
Annotation database (184 Mb)
* Annotation Database
Test data set for breast cancer cell-line SK-BR-3 (673 Kb)
* Test Data