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Genome Biol. 2011 Aug 11;12(8):R72. doi: 10.1186/gb-2011-12-8-r72.

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.

Author information

1
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA. infphilo@umiacs.umd.edu

Abstract

TopHat-Fusion is an algorithm designed to discover transcripts representing fusion gene products, which result from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. TopHat-Fusion is an enhanced version of TopHat, an efficient program that aligns RNA-seq reads without relying on existing annotation. Because it is independent of gene annotation, TopHat-Fusion can discover fusion products deriving from known genes, unknown genes and unannotated splice variants of known genes. Using RNA-seq data from breast and prostate cancer cell lines, we detected both previously reported and novel fusions with solid supporting evidence. TopHat-Fusion is available at http://tophat-fusion.sourceforge.net/.

PMID:
21835007
PMCID:
PMC3245612
DOI:
10.1186/gb-2011-12-8-r72
[Indexed for MEDLINE]
Free PMC Article

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